Cosumnes Phase 2

This project continued the monitoring of basic ecological and hydrological processes, but expanded to include investigations of: patterns of restoration success, groundwater and vegetation interaction, linking aquatic and terrestrial ecosystems, bird populations as indicators of ecosystem integrity, and data management for ecosystem monitoring.

Cosumnes I focused primarily on the relationship between hydrologic conditions and aquatic ecosystems.

Cosumnes II, also funded by CBDA/CALFED, built on this earlier work, but emphasized the connection between aquatic and terrestrial systems in floodplain environments.

This project continued the monitoring of basic ecological and hydrological processes, but expanded to include investigations of: patterns of restoration success, groundwater and vegetation interaction, linking aquatic and terrestrial ecosystems, bird populations as indicators of ecosystem integrity, and data management for ecosystem monitoring.

The Cosumnes 2 phase of the project ended in 2004. Reports and papers are posted within the report, and in the CRG2 Reports and Publications section.

Executive Summary

The Cosumnes River Experience and Recommendations for Restoration Monitoring

Floodplains are among the most productive and diverse ecosystems on Earth and are now being recognized globally for the ecosystem services they provide; however, they are also one the more impacted ecosystems globally and are at risk of further degradation by a fusillade of anthropogenic stressors and consumptive demands. Natural floodplain ecosystems are a product of, and adapted to, highly variable hydrologic regimes – typified by droughts, catastrophic floods, and frequent periods of inundation - expressed across seasonal, yearly, and decadal dimensions. This hydrologic variability acts to reset various biotic populations within aquatic, riparian, and wetland ecosystems through disturbance, acting as an essential ecological process in maintaining complex ecosystem pathways. Multipath ecological relationships, expressed as trophic food webs or transition states, promote high biodiversity and biological integrity. In floodplain ecosystems, these ecological relationships are underpinned by the fundamental linkage between floodplains and river systems, forming a critical linkage that creates and maintains a mosaic of habitats for groundwater recharge, primary productivity and biogeochemistry, the reproductive cycle of fishes, nesting and foraging of birds, and regeneration of riparian vegetation.

It is estimated that less than 5% of the Central Valley’s original riparian forest remain intact. This fact, coupled with the simultaneous loss of floodplain wetlands to channel modification, agriculture and urbanization, has resulted in the desire for ecosystem scale restoration. For Central Valley lowland river floodplains, the only cost-effective method for large scale restoration is semi-passive; in essence, through structural modification – such as levee breaches or levee setbacks, followed by natural succession of flood dependent ecological communities – where nature does most of the work. However, past semi-passive restoration efforts have not been uniformly successful either in generating high quality, productive native-dominated vegetation or in reestablishing functioning food webs supporting floodplain sentinel species (e.g.,birds, fishes, etc.). The lower Cosumnes River floodplain provides an unprecedented opportunity to examine semi-passive restoration techniques in relation to successional trajectory and opportunities for improved management and also the development of monitoring methodologies, as there is a 20-year history of wetland and riparian habitat restoration – both active and semi-passive in technique – that allows for temporal and comparative analyses.

To help elucidate important patterns and processes in semi-passive restoration, we examine the interaction and feedback pathways between the physical regime and the ecological communities in the Cosumnes River floodplain, which is created and maintained by a natural hydrologic discharge regime that promotes habitat heterogeneity, nutrient transformation and exchange, and spatiotemporal fluxes in productivity. Other important pathways include the interactions between the hydrologic discharge regime and groundwater, subsequent effects of groundwater on establishment of riparian forests, and possible changes in groundwater regime caused by forest evapotranspiration. In turn, forest productivity and structure provide both a trophic and a structural basis for both aquatic and terrestrial productivity, wherein biological indicators such as birds respond to the mosaic of qualitative and quantitative differences created by the differential effects of ecosystem disturbance and restoration.

Freshwater ecosystems, including floodplain and riparian habitats, are among the Earth’s most productive and diverse ecological systems providing innumerable services to humans. In addition to these ecosystem services, such as water supply, freshwater ecosystems have productive floodplain and riparian habitats that are essential for sustaining and recovering at-risk resident and migratory populations of native plants and animals. A challenge for floodplain restoration and management in California’s Bay-Delta, which is heavily populated by humans and used for agricultural production, is to configure floodplains and their food webs so that populations of beneficial species thrive. As we restore and manage riparian zones and floodplains, we need to learn how their spatial and temporal characteristics affect ecological function and processes, so we can sustain their ecological services. From our studies, presented here, we understand that natural floodplain ecosystems are a product of, and adapted to, highly variable hydrologic regimes. It is important that the general public, and resource managers, understand and adapt to a hydrologic regime that is typified by droughts, catastrophic floods, and frequent periods of inundation. Our studies document that hydrologic variability is expressed across seasonal, yearly, and decadal units of time, but is also changing its mode. Therefore, restoration and management that uses hydrologic variability to reset various biotic populations through disturbance, must be cognizant of the alternate trajectories that may occur. Understanding the multiple ecological paths, expressed in our studies asphysical processes governing trophic food webs, will also allow us to consider long-term consequences to biodiversity and biological integrity.

Using the Cosumnes River floodplain ecosystem as a living laboratory, our studies focused on the ecological relationships that form critical linkages between and maintain a mosaic of habitats for groundwater recharge, primary productivity and biogeochemistry in floodwaters, reproductive cycle of fishes and resulting communities, nesting and foraging of birds, the presence and utilization of bats, as well as the continued regeneration of riparian vegetation. The Cosumnes River Preserve and the river itself has provided us – in part due to its unimpaired flood flow regime maintained by its undammed status – with the unique opportunity to study two approaches to restoration. Passive restoration, defined as letting the ecosystem self-organize following early intervention, clearly affects larger are with less monetary investment. Active restoration, the continued and direct manipulation of ecosystem members and process, does provide more certainty in short-term effects. Thus, this study and the preceding ones have benefited from the implementation of both restoration methods to study restoration success metrics. There are clear ecological benefits to passive restoration, accomplished through floodplain reconnectivity, through increases in structural complexity and subsequent functional diversity, which in turns gives rise to increased biodiversity through creating additional pathways for species interaction and energy transfer and transformation. From our studies, we emphasize the importance of large floods which can export large woody debris and coarse particulate organic matter from the floodplain to the channel, creating habitat, and creating important avenues for energy transfer across and within the river-floodplain system.

1. Flood Regime

Flood Regime Summaries

Characterizing Hydrologic Variability of the Cosumnes River Floodplain

This study characterizes the hydrologic variability of the lower Cosumnes River by analyzing a 98-year streamflow record (1908 – 2005). We develop a flood regime classification methodology by separating similar water year types and similar flood types based on magnitude, duration, and timing.

Nutrient and food resource fluxing through the river floodplain system: An analysis of flood pulse phases as a control on patch dynamics across a restored floodplain.

The objectives are to quantify the flux of nutrients and food resources across the channel-floodplain boundary while delineating the chemical and hydrological signature of different stages of the flood pulse, and to study the influence of the flood pulse on the spatial distribution of suspended algal biomass across the surface of a restored floodplain.


Flood Regime - Variability

Characterizing Hydrologic Variability of the Cosumnes River Floodplain

Eric G. Booth


  1. Characterize the hydrologic variability of the lower Cosumnes River by analyzing a 98-year streamflow record (1908 – 2005).
  2. Develop a flood regime classification methodology by separating similar water year types and similar flood types based on magnitude, duration, and timing of flooding.


The Cosumnes River watershed, located southeast of Sacramento, drains a 1989 km2 area starting at 2300 m in the Sierra Nevada mountain range and draining into the Mokelumne River at an elevation of 2 m above sea level. Water from the Cosumnes River ultimately flows into the San Francisco Bay – Delta. It is one of the few unimpounded rivers flowing from the Sierra Nevada Range into the Central Valley. With the exception of loss of base flow in the summer and fall (Fleckenstein et al. in press), the Cosumnes maintains a relatively unimpaired hydrograph.


A continuous daily record of discharge data (Figure 3) for the Cosumnes River at Michigan Bar (MHB) from 1908 – 2005 was acquired from the U.S. Geological Survey’s National Water Information System. The MHB streamflow record was analyzed for stationarity because many surrounding basins in the Sierra Nevada exhibit trends in variables such as center of mass of annual flow and maximum annual flow due to changes in climatic conditions since 1950. Several hydrogeomorphically significant thresholds for flood magnitude and duration were developed in order to classify flood events. 10 flood types were created based upon the thresholds and the frequencies at which they occurred throughout the record were calculated. These flood types were then used to develop distinct water year types and their frequencies were calculated.

Key Findings:

  1. The Cosumnes River floodplain experiences two distinct periods of flooding. The first period, occurring roughly from November to February, is comprised of floods that tend to be flashier and have larger peak flows but sustained flooding is not as common during this period as in the second period. The second period, occurring roughly from March to May, contains smaller peak flows compared to the first period but days of flooding are more abundant. These two distinct periods of the flood season are most likely due to later-season snowmelt contributions and larger shallow groundwater inputs in the second period from sources earlier in the season.
  2. This bi-seasonal effect is also reflected in the difference in mean start date for certain flood types – the flood types with larger flood magnitudes and relatively small durations occur early in the season while flood types with longer flood durations and relatively small magnitudes occur later in the season.
  3. Flood types 2 and 3, which consist of the floods that can transport sand onto the floodplain, occur at least once in approximately two out of every three years and twice in half of the years. The very large magnitude type 3 floods occur at least once in one out of every five years on average. The long duration flood types (L and V) occur at least once in roughly six out of every ten years.
  4. The flood type classification along with the flood statistics determined for each of the 479 flood events on record can also be used to test the potential long-term frequency of certain biological phenomena observed on the lowland Cosumnes River floodplain such as the “productivity pumping” described in Ahearn et al. (in review). Based on historical data, at least one productivity pump flood occurred, on average, in two out of every three years, and at least two effective floods occurred in roughly half of the years.
  5. The water year type classification also has the ability to analyze the frequency of certain ecological phenomena but on an annual time-scale. As an example of this connection, Water Year Type (WYT) 7 contains at least one M3 flood, which will most likely create new bare ground in the form of sand deposits, and substantial late-season flooding. Using the Recruitment Box Model (Amlin and Rood 2002), the combination of new bare ground and late-season flooding provides a very favorable condition for the recruitment of cottonwood trees. However, more research is needed to more acutely describe the ecological differences between water year types.
  6. The distribution of certain water year types throughout the period of record also illuminated the previously mentioned observation of the inconsistency of certain aspects of the streamflow record with a stationary time series. WYT-3, a year with a relatively dry winter but a relatively wet spring, decreased in frequency in the second half of the streamflow record (post-1956). In contrast, WYT-6, a year with a very wet winter but a relatively dry spring, increased in frequency in the second half of the record. These two opposite trends are consistent with the hypothesis of a rising snow-rainfall transition line, leading to larger winter floods and diminishing the later snowmelt-dominated part of the hydrograph due to increased winter and spring air temperatures since the mid-20th century (Stewart et al. 2005).

Recommendations for management & monitoring:

As more complex water resources issues surface in the future, managers need to be informed of the degree of hydrologic variability that aquatic ecosystems critically need for them to continue to provide ecosystem services to humans. Organizing flood events and water years into similar types will allow managers to visualize this variability more effectively. While climate will ultimately drive the frequency at which these important floods occur, as a watershed becomes more regulated the water managers will increasingly become more responsible for maintaining the natural frequencies of specific flood types and water year types. A wide-range of hydrologic events are responsible for maintaining the ecological integrity of aquatic ecosystems by resetting ecological succession during large floods, providing ecological cues, and discouraging the persistence of non-native species that are not adapted to natural conditions (Stewardson and Gippel 2003). By knowing roughly what the natural frequencies of specific flood types and water year types were in the recent past, water managers will be able to more accurately provide these aquatic ecosystems with the variability they require to exist.

Flood Regime - Water Chemistry

Nutrient and food resource fluxing through the river floodplain system: An analysis of flood pulse phases as a control on patch dynamics across a restored floodplain

Dylan S. Ahearn


  1. Quantify the flux of nutrients and food resources across the channel-floodplain boundary while delineating the chemical and hydrological signature of different stages of the flood pulse.
  2. Study the influence of the flood pulse on the spatial distribution of suspended algal biomass across the surface of a restored floodplain.


The study site was located 34 km south of Sacramento, CA on the lower Cosumnes River, approximately 5.5 km upstream from the confluence with the Mokelumne River (Fig. 1). In 1997, four breaches were cut into the levee bordering the eastern edge of the channel. Two inlet breaches (Tn and Ts) allow river water to enter the 36 ha restored floodplain during floods. Mean flood transit time across the floodplain in 2005 was approximately 1 day; during which time the floodplain held an average of 90 000 m3 of floodwater. After traversing the floodplain, water egresses through two exit breaches (Te and Tw). Mean discharge across the floodplain in 2005 was 6.09 m3 s-1, while during this same period mean discharge in the main channel (as measured at USGS gage #11335000) was 37.1 m3 s-1.


Between December 2004 and June 2005, samples were collected with ISCO 6700 autosamplers at Tn, Te, and Tw. Water Quality at Ts was assumed to be identical to Tn chemistry. Samples were analyzed for Chl-a, DOC, TIN, TP, TDS, TSS, and VSS. Additionally, a YSI 6600 multiparameter sonde (temperature, pH, TDS, Chl-a, turbidity) with GPS capabilities was employed to collected data at an average of 120 sites across the surface of the floodplain. The autosamplers collected samples during flooding events on a 2-hour time-step. During the 172 days of flooding, 175 samples (169 matched pairs) were collected from each of the three sites. During this same period monitoring of the surface waters of the floodplain was conducted on 22 separate occasions.

Key Findings

  1. Our analysis indicates that periodic connection and disconnection of the floodplain with the channel is vital to the functioning of the floodplain as a source of concentrated suspended algal biomass for downstream aquatic ecosystems.
  2. Peak Chl-a levels on the floodplain occurred during disconnection, reaching levels as high as 25 µ?g l-1. Chlorophyll-a distribution across the floodplain was controlled by water age and local physical/biological conditions, the latter of which were primarily a function of water depth.
  3. During connection, the primary pond on the floodplain exhibited low Chl-a (mean = 3.6??g µl-1) and the shallow littoral zones had elevated concentrations (mean = 5.2 µ??g l-1); during disconnection, the shallow zones Chl-a increased (mean = 11.2 µ??g l-1), but the pond experienced the greatest algal growth (mean = 14.2 µ??g l-1).
  4. Storm-induced floodwaters entering the floodplain not only displaced antecedent floodplain waters, but also redistributed floodplain resources, creating complex mixing dynamics between parcels of water with distinct chemistries. Incomplete replacement of antecedent floodplain waters led to localized hypoxia in non-flushed areas.
  5. The floodplain was an annual sink for all constituents measured (total suspended sediment (TSS): 372 Mt ha-1 yr-1, volatile suspended sediments (VSS): Mt ha-1 yr-1, total inorganic nitrogen (TIN): 0.43 Mt ha-1 yr-1, DOC: 3 Mt ha-1 yr-1, and Chl-a: 0.01 Mt ha-1 yr-1) but closer analysis revealed that some small flooding events caused net DOC and Chl-a export from the floodplain.
  6. Partitioning of the phases of the flood pulse revealed three physically and chemically distinct stages: the flushing phase, the transport phase, and the draining phase. The flushing phase was a brief period of export on the rising limb of the flood, this phase only occurred after an extended period with no upstream connection. The transport phase dominated the flux balance of the system and was marked by retention of all the measured constituents on the floodplain. The draining phase began when outflow from the floodplain exceeded inflow, this phase was an export phase for both DOC and Chl-a.
  7. The fact that small floods were not dominated by the retentive transport phase helps explains why these floods tended to cause net export, rather than retention, of materials on the floodplain.
  8. We propose the notion of “floodplain proportional flooding” for restored floodplain systems, whereby flood size should not overwhelm floodplain volume. In this way residence time is increased as is the potential for the floodplain to be a source for DOC and phytoplankton, valuable food resources for downstream aquatic ecosystems.
  9. The degree of complexity revealed in this analysis makes clear the need for high-resolution spatial and temporal studies such as this to begin to understand the functioning of dynamic and heterogeneous floodplain ecosystems.

Recommendations for management & monitoring

If a primary goal of future floodplain restoration is to create an additional source of food resources for downstream aquatic systems then we recommend “floodplain proportional flooding”, whereby the median flood size does not overwhelm the capacity of the floodplain. Such flooding will assure high MRT on the floodplain for at least one half of the annual floods and thus increase export of DOC and phytoplankton. Given this we must also note the importance of large floods which can export large woody debris and coarse particulate organic matter from the floodplain to the channel, these are also important avenues for energy transfer across the river-floodplain system. Previous studies that have monitored the flux of materials across the channel floodplain boundary have used a relatively coarse sampling strategy. This study has shown that there exist biogeochemically distinct phases to the flood pulse and heterogeneous algal biomass distribution across the floodplain which can not be quantified without high resolution sampling. As such, we recommend intensive sampling in both space and time in order to characterize dynamic and heterogeneous floodplain ecosystem.

Flood Regime Characterization (FRC) for Matlab

This program is an attempt to transform the methods discussed in the companion paper into a portable computer program so that they can be used by researchers and managers on other watersheds in order to characterize a flood regime. The main inputs to the program are a daily streamflow record and a set of flood duration and magnitude thresholds that have some meaningful connection to the hydrologic, geomorphic, and/or ecological processes in the specific watershed. The main outputs are a list of floods, flood types, and water year types along with useful statistics for each list and estimates of the frequency of each flood type and water year type.

Downloads & Resources

  • Program manual (PDF 300KB)
  • Program source code (ZIP 20KB)
  • Example output for Cosumnes River (ZIP 250KB)
  • Link to companion paper (Link)

2. Floodplain Restoration

Floodplain Restoration Success Criteria and Monitoring

Joshua H. Viers
Ingrid B. Hogle
James F. Quinn

Preface of study task intent

To better understand how restoration of riparian vegetation is influenced by a variety of factors, such as physical processes, especially inundation, and the multiple methods of restoration (both active and semi-passive) that land managers have used in the Cosumnes floodplain, we developed four complementary approaches to addressing different facets of assessing restoration outcomes. Embedded within this overall objective, we are interested in understanding of the spatial dynamics inherent to riparian vegetation across multiple scales, and how this information can help inform restoration efforts in the California Bay-Delta region.

Our studies were designed to help answer outstanding questions concerning landscape-scale physical factors that either promote or diminish restoration success, and how these factors can be modeled to identify potential restoration sites for future investments. Further, the differences between semi-passive restoration (i.e., breaching levees, restoring floodplain connectivity) and active restoration (planting trees, intensive management) are largely untested over large areas. As a result, an important goal was to document the underlying differences among sites treated with semi-passive versus active restoration implementations. As non-native invasive plants often disrupt and become the limiting factor in long-term success of restoration efforts, we began an ongoing process of assessing how non-native plant invasions are affected by physical and environmental site characteristics found in semi-passive restoration areas.

General background on study system

Riparian vegetation is a key habitat in California’s Central Valley, and one that is much diminished from historical distribution. Riparian habitats, including terrestrial vegetation and freshwater aquatic ecosystems, are impacted by a number of anthropogenic activities and have been identified as a restoration priority for the California Bay-Delta Authority and many conservation organizations, such as The Nature Conservancy. The Cosumnes River Preserve is using two different approaches to restoration of the riparian zone and floodplain ecosystem. One method is the active planting of tree species. Active restoration provides some control over the composition of incipient forests, but it is also localized, labor-intensive, and bypasses natural successional processes. The other approach is semi-passive in the sense that certain manipulations, such as breaching levees, are intended to promote “natural” fluvial processes to the floodplain and thus provide a vector for the natural re-establishment of riparian forests.

The restorative impact of levee breaches and setbacks can cover large areas and emulate natural floodplain processes, but there is no guarantee that re-vegetation will favor native species or restore a desirable mix of habitat structures. Active planting of native species may help to “jump-start” revegetation towards desired species assemblages, but restoration methods are still being developed, with highly variable results throughout the Preserve. Additionally, the invasion of exotic species such as perennial pepperweed (Lepidium latifolium) into both active and passive restoration areas threatens the establishment and maintenance of native species, and presents an ongoing management challenge.

The Cosumnes River Preserve encompasses myriad individual land parcels, which are subdivided into restoration sites subject to unique environmental conditions and management histories. Differences between sites include variable soil characteristics, hydrology and restoration methods employed. Restoration efforts have been erratically documented and monitored over the history of the Preserve, making analysis of the relative success of different restoration techniques a difficult task. Variables in active restoration techniques include species planted, type of planting, frequency and amount of summer irrigation, and soil manipulation (disking, scraping, etc.). Hydrology ranges from uplands to restored floodplains, and soils range from deposited sand splays to shallow claypans to deeply tilled former agricultural fields with good drainage.

Brief methods

The first phase of our study focused on identification of physical factors such as location of water bodies, soil type, flood frequency, and elevation change from nearest waterbody in relation to individual sites in order to inform models of restoration opportunities. Keller and Quinn extend a raster-based GIS to include physical conditions that affect riparian community growth and establishment. The resultant models relate restoration potential to physical parameters including flood frequency, distance from the nearest body of water, change in elevation from the nearest body of water, maximum soil permeability, and a calculated wetness index.

The second phase of our study was dedicated to assembling a robust collection of riparian plant species present at the Cosumnes River Preserve and comparing it to other Central Valley riparian systems at differing scales. By using a nested analysis, Viers et al. were able to document known and expected rates of species diversity as expressed by local and regional measures. This analysis provides a quantitative framework for evaluating the degree to which a restoration site, such as the Cosumnes floodplain, can capture regional biodiversity as opposed to reflecting unique on-site biological values. By calculating regional rates of plant diversity in comparison to local ones, we can identify any potential deficiencies and promote them as targets for future conservation and restoration efforts.

The final two phases of our study used GIS geodatabase technology to assemble and analyze spatial and empirical environmental data at the species, population, and site level. This included conducting a retrospective analysis of riparian restoration monitoring, and monitoring the extent of a non-native invasive species on the experimental floodplain. In order to evaluate environmental conditions present on the Cosumnes River Preserve, we compiled and collected information on site characteristics and vegetative change in all active and passive restoration areas. We used aerial imagery to track changes in areal tree cover extent in restoration areas over time. We incorporated all known restoration records over the 20 years of active and passive restoration at the Preserve (1985 – 2005) into a geodatabase. Lastly, we monitored the invasion of perennial pepperweed, a non-native herb which threatens to create monocultures in riparian systems, on a restored floodplain from 2002 through 2005. We analyzed vegetative change in restoration sites for correlation with this and other site conditions including distance from water bodies, soil type, flood frequency, and elevation change from nearest waterbody.

Key findings

Keller and Quinn found that 72% of all riparian forest is within 100m of the active Cosumnes River channel, and that flood frequency and distance to water features were the strongest predictors of historical riparian forest distribution. Valley oak establishment success and growth rates varied considerably among restoration sites, suggesting that on a coarse scale, passive restoration approaches may be most suitable for re-establishing valley-oak riparian forests adjacent to channels where they presumably were concentrated prior to agricultural land-clearing.

In examining regional plant species diversity and rates of turnover in relation to localized ones, Viers et al. found that herbaceous species are more important than woody species in driving localized diversity measures. These results stem from the observation that riparian woody species, including trees such as valley oak, cottonwood, and willows, are largely cosmopolitan in the California Bay-Delta region.

Retrospective analysis of restoration site monitoring data was a particular challenge due to the dearth of information; however, findings from this study phase indicate that hydrologic regime, disturbance processes, soil composition, and to a limited degree management prescriptions drive active restoration success as measured by germination, seedling survival, and growth rates.

In the course of the study, we assembled a data framework that attempts to integrate plant population data from scientific and management information collected by multiple organizations, projects, and investigators. Unfortunately, we found numerous data gaps in our collection of riparian restoration monitoring data, which spans 20 years and covers much of the Cosumnes River Preserve proper. For example, we found that many datasets were grossly incomplete for most years; species identifications were inconsistent, for example, confusing the identification of several willow species with more than one common name; there was no systematic recording of volunteer species establishment within active or semi-passive restoration sites; and there were no exact locations recorded for many restoration activities. All necessarily coarsened our analytical approach, but the data framework developed may serve as a model for future, more complete, restoration monitoring data management.

Among invasive plant species, we concentrated on analysis of the population dynamics of perennial pepperweed, a non-native invasive species that is becoming established in the Cosumnes River experimental floodplain, and that has become the invader of most concern to the land managers due to its threat to native plant diversity. We have found that the initial establishment and subsequent spread of pepperweed populations are promoted by disturbance and site characteristics similar to those favorable to emerging riparian forest, such as soil moisture and nutrients.

Recommendations for management and monitoring

Active restoration of riparian forests and floodplains is time-consuming and expensive, reliable methods are not yet established, and end results are highly variable with limited explanatory power. For this reason, we feel that riparian and floodplain restoration efforts should focus on re-establishing diverse river functions, such as ecological succession and hydrologic connectivity between surface and subsurface waters. Not only do semi-passive restoration techniques cover larger areas for far less investment, the incipient ecological processes that accompany the re-establishment of hydrological functions create habitat mosaics beneficial to many upper-trophic level species and promote staged successional trajectories that are the embodiment of structural and functional diversity. At the end of the day, biodiversity is dependent upon underlying physical complexity, which in the case of California’s riverine floodplains, is created by hydrologic variability created by a natural flow regime.

Spatial models are an informative mechanism to both gauge ecosystem processes and to leverage future restoration planning. The advent and utilization of geographical information systems allows for continual model improvement and rapid re-analysis of particular scenarios useful for resource management and decision making. That being said, however, it is still difficult to acquire the requisite validation data for many models. Data from recent meter-scale lidar and hyperspectral acquisitions will improve future modeling efforts. These data are expensive to acquire and process, but provide the most realistic method for monitoring species-level change over large passive restoration efforts (e.g., through levee setbacks or breaches) over the California Bay-Delta region. Such data are limited to the last several years; however, we foresee that these data will serve as baseline information for future analyses as these and other technologies become more common and affordable.

We found many data missing from the 20 year history of restoration on the Cosumnes River Preserve, making retrospective analyses difficult. We advocate standardized data frameworks and meaningful metadata – those descriptive data that detail the type, form, and nature of collected information – be required with all programmatic monitoring efforts, such as those mandated by resource agencies or funded by regional governments. Future analyses will want to capitalize on new statistical methods, including the information-theoretic approach, with its explicit model specification, and longitudinal data analysis, which is specific to repeated measures in irregularly spaced time events.

We studied the invasion of a non-native plant onto the Cosumnes River experimental floodplain to help determine, which, if any, landscape factors promote its invasion. As part of this process, we followed its population dynamics to better understand its habit. Understanding the invasion process, especially the phases of introduction, colonization, and naturalization, helps determine appropriate remediation. Weeds typically spread through a two-phase increase with an initial lag followed by exponential increase, or an immediate exponential increase. The type of expansion trend exhibited is important for weed control strategies in that it helps gauge the amount of time available to leverage resources against the invasion. Based on four years of monitoring, areal expansion of established patches of perennial pepperweed at our site appears to be following a pattern of exponential growth, generally irrespective of floodplain position. New patches tend to In addition to further research on the ecology of perennial pepperweed, we recommend early eradication of emerging populations.

Populations of Lepidium latifolium are increasing rapidly in the Cosumnes River Preserve’s restored floodplain, with only minor variability in rate of spread across the landscape. Introductions appear to be from both roads and breaches, and have the potential to spread quickly and dominate open areas and the understory of the rapidly expanding floodplain forests. Although we found that perennial pepperweed patches were most likely to be eliminated in large flood events, relying on scour and deposition to control pepperweed populations is not advised; pepperweed patches need to be within 16m of an active inflow levee breach to have greater than a 50% chance of being completely destroyed.

Control measures should be implemented and evaluated to slow the expansion of this invasive species so as to allow the natural succession of native species in this restored floodplain. Experimental control methods are currently being tested, and will inform adaptive weed management programs at the Preserve. Concurrently, ground-based inventories of management sites are underway. We recommend continuation of these two efforts, and encourage the use of advanced spatial technologies to identify coarser-scale establishment and subsequent spread over time. The use of such technology for non-native species mapping is now robust, and can be used to generate inventory maps for prioritization of control efforts over large spatial areas. Other recommendations for management and monitoring of Lepidium include the development of probability surface models that predict future invasion; such models should be based on statistical relationships between relevant factors, such as elevation, distance to disturbance vector, and proximity to former invasion. These models can be correlated with remotely sensed imagery, and derivative measures of plant vigor, to provide a more synoptic view of Lepidium invasions that can be applied to other areas within the California Bay-Delta region.

We recommend the use of high spatial resolution remote sensing for extensive monitoring of riparian forests and invasive plant species. Advances in the use of lidar – light detection and ranging or laser altimetry – and hyperspectral sensors have reduced the resolution of most data products to better than 1m on the ground. Lidar provides detailed structural measurements – often more than seven laser measurements per square meter that are better than 10cm in vertical accuracy – that can be constructed to depict microtopographic relief and plant canopy structure over thousands of hectares. Hyperspectral imagery allows for the identification of many constituents, such as flowering non-native species or dead and dying trees, in addition to geomorphically important substrates such as sands and gravels. These types of remote sensing can be conducted on fixed intervals (e.g., yearly) or during time sensitive events (e.g., floods) as a robust form of monitoring.

.pdf version of complete summary


3. Groundwater

Groundwater Vegetation Interactions Summaries

Water Budget Analysis Summary

This study task develops a hydrologic model for a river-reach and floodplain area of the Cosumnes River for estimating water budget components, including channel, vadose zone, and bank storage, riparian evapotranspiration, and aquifer recharge. The hydrologic model was designed to establish the presence of perched aquifer systems at the Cosumnes River that may function to buffer near stream ecosystems from drought. The model provides quantitative analyses of many of the key characteristics governing perched groundwater hydrology, providing insights about processes as well as the foundation for future studies.

Evapotranspiration Analysis Summary

The intent of this study task was to measure riparian evapotranspiration at two different sites within the Cosumnes watershed. In conjunction with the groundwater and hydrology group, this study estimated the amount of water lost from the hydrologic budget via evapotranspiration and likewise observe the effect of groundwater availability on riparian ecosystem evapotranspiration.


Groundwater Summary

Water budget analysis for a river-reach/floodplain area and the influence of a shallow perched aquifer system


  1. Develop a hydrologic model for a river-reach/floodplain area of the Cosumnes River for estimating water budget components, including channel, vadose zone, and bank storage, riparian evapotranspiration, and aquifer recharge. The hydrologic model was designed in light of the presence of perched aquifer systems at the Cosumnes that may function to buffer near stream ecosystems from drought.
  2. Provide quantitative analyses of many of the key characteristics governing perched groundwater hydrology, providing insights about processes as well as the foundation for future studies.


Previous hydrologic studies have developed geologic models of the alluvial aquifer systems surrounding the Cosumnes River based on hundreds of driller’s logs for the basin (Fleckenstein et al., 2006). These data indicate that the river flows over highly heterogeneous sediment deposits that influence how the river responds to pumping-induced water table decline. The present work builds upon previous investigations that suggest mixtures of sand bodies and low-permeable silts and clays can result in perched aquifer systems and local mounding of the regional groundwater to the level of the river surface. A smaller and more complex model is developed in the present study as compared with the model presented by Fleckenstein et al (2006) to consider finer-scale field observations of geology and other hydrologic parameters. The model is developed for a 200 m reach located in the lower section of the river where it flows beneath State Highway 99 in Sacramento County just above the McConnell stream gage. The study reach contains a 100 m long and 600 m wide floodplain area that floods to various extents during most years; however, the floodplain drains quickly following inundation. The floodplain area supports patches of riparian vegetation not present in adjacent areas where the river is confined between constructed levees.


Between December 2002 and Dec 2004, Continuous measurements of river and regional groundwater levels were made on an hourly basis. Additionally, sediment water content and temperature were made on an hourly basis to depths between 7-10 m beneath the river and floodplain areas. Detailed lithologic descriptions of sediment were made from 17 boreholes drilled in the study area. Evapotranspiration was measured using an energy-balance method from willows trees growing along the Cosumnes River (J. Korchendorfer and K. T. Paw U, written communication, 2004). These data were used to calibrate a three-dimensional variably-saturated non-isothermal flow model. Sediment heterogeneity was represented in the model using transition probability-based geostatistical approach. A spatially-distributed demand driven/supply limited root uptake model was also incorporated into the model.

Key Findings:

  1. Our analysis indicates that perched aquifers form beneath the Cosumnes and have a significant influence on the hydrologic budget surrounding the river. Perched aquifers near the river correspond to patches of riparian vegetation not present in adjacent areas along the river.
  2. Profiles of sediment water content measured beneath the floodplain indicate that 6-m thick saturated regions (perched aquifers) form beneath the floodplain due to inundation followed by slow desaturation during months of high evapotranspiration. Portions of the vadose zone maintain high saturation throughout the dry season (July-September) following floodplain inundation due to low-permeable sediment layers.
  3. Perched aquifers can shift the water budget near the river by maintaining saturated conditions within the riparian root zone, which allows water seeping from the river to be lost as evapotranspiration rather than seeping back to the river or to regional aquifers. The model predicted a 50% increase in ET losses due to the presence of perched aquifers when water availability was used as an indicator of riparian vegetation.
  4. The model predicted that perched groundwater within the study area provided 0 to 7 m3/d of baseflow to the river; however, baseflow contributions declined shortly following the decline of inflow upstream of the study area (early June). Decline of perched aquifer seepage to the river adjacent to the floodplain is attributed to the breached levee in the study area, which results in lower perched aquifer levels adjacent to the river as compared to other areas with steep riverbanks (levees).
  5. Hypothetical modeling of perched aquifer systems near a river indicate that perched aquifers can provide significant baseflow to a river (700 to 4300 m3/d) for variety geologic and geomorphic conditions. Conditions favorable for enhancing baseflow from perched aquifers are high contrasts in hydraulic conductivity between the perching unit and overlying coarser sediment. These conditions are considered likely to occur at the Cosumnes based on field observations. These results indicate that perched aquifers may be important for maintaining minimum flow levels for migrating Salmon at the Cosumnes.
  6. Riparian vegetation may diminish baseflow contribution from perched aquifers by as much as 30% where a thick riparian forest exist adjacent to the river and where the riparian root zone extends below the elevation of the channel surface. Tall river banks (levees) can result in a channel bottom elevation that is lower than the riparian root zone, such that perched aquifer systems drain into the channel instead of being lost as ET.

Recommendations for management & monitoring:

Management of perched aquifers may enhance river baseflow for migrating salmon and other in-stream biota. Additionally, perched aquifers may be managed to increase the riparian area around the Cosumnes; however, as described increased ET due to riparian vegetation may diminish baseflow. Thus, management of perched aquifers should consider whether the goal is to enhance baseflow for migrating salmon or for restoring riparian forests adjacent to the river. Management of perched aquifers could be done through artificial recharge during periods of water surplus. Perched aquifers could be recharged by releasing water down the channel from Folsom South Canal, by breaching levees to cause floodplain inundation, and by irrigating agricultural fields adjacent to the river. Most important, however, would be to continue field investigations to locate areas favorable for the development of perched aquifers and mounded regional groundwater levels that enhance river baseflow such that management of perched aquifer systems could be maximized.

Evapotranspiration in a Riparian Canopy

Evapotranspiration Analysis

KyawTha Paw U
John Kochendorfer

Preface on study task intent

Our primary intent in this study was to measure riparian evapotranspiration at two different sites within the Cosumnes watershed. In conjunction with the hydrology group, we were to estimate the amount of water lost from the hydrologic budget via evapotranspiration and likewise observe the effect of groundwater availability on riparian ecosystem evapotranspiration.

General background on study system

Restored riparian areas including vegetation regeneration needs to be monitored to determine the effects of restoration efforts. A major determinant of restoration involves hydrological cycle modification for the sites. To understand the effects of the hydrological cycle changes, the cycle itself must be studied in depth. Groundwater and vegetation interactions are substantially affected by evapotranspiration dynamics. Our sub-task was to quantify evapotranspiration at two sites, where other data were being gathered by hydrological researchers.

Operational hypotheses

Evapotranspiration from riparian vegetation is greater than that for other dryland ecosystems.

Narrow bands of riparian vegetation (along side streambeds) evapotranspire at higher rates than more extensive riparian forest ecosystems.

Brief methods

At the upstream, Deer Creek Costello site we used an infra-red surface temperature/ aerodynamic resistance method that we developed for use in this riparian area of narrow fetch. Our technique allowed us to estimate the amount of evapotranspiration occurring at the upstream site by measuring surface temperature of the ecosystem (Ts), net radiation (Rn), air temperature (Ta), relative humidity, and ground heat flux (G). Using these direct measurements we estimated the sensible heat flux (H) and the only remaining important unknown component of the energy budget was latent energy (LE), from which evapotranspiration can be calculated directly. The energy budget of the ecosystem is expressed as follows:

LE is solved for as a residual, and converting LE from units of energy (W m-2) to units of mass or volume of water is trivial. The most challenging part of this technique involves estimating aerodynamic resistance (rh) as a function of wind speed. Our approach was to solve for rh under simplified conditions, describe this aerodynamic resistance as a function of wind velocity, and then use this estimated resistance value to calculate LE at ½ hour intervals during times when we cannot measure rh.

At the Accidental Forest site we used eddy-covariance to measure the exchange of sensible heat, water vapor, and carbon dioxide with the atmosphere. Using a fast response three dimensional sonic anemometer and a fast response infrared gas analyzer we measured wind speeds and gas concentrations ten times per second. We then calculated the covariance between the vertical wind speed and the temperature or the gas concentrations, including a correction for the changing density of the air moving through the gas analyzer. Under ideal conditions these covariances calculated every half-hour are equal to net exchange with the atmosphere. The half hour covariances were screened for times when conditions are far from ideal, such as when very stable micrometeorological conditions suppress turbulence or when winds are from directions with low fetch, and this data were removed from the reported results and when the gaps were small the data were replaced using adjacent half hour results.

The complete budget equations involve water vapor exchange caused by both mean flows and the turbulent component of flows. Over a volume of air sampled by micrometeorological sensors, the full equation would be:

where the ET is expressed as a mass flux density, ρ is the dry air density (kg m-3), s is the humidity as a mixing ratio (kg H2O per kg dry air), ρω is the absolute humidity (kg water vapor per cubic meter), u is the horizontal wind velocity along the mean wind direction, ω is the vertical wind velocity, the overbars indicate ensemble or time averaging, and the primes (') indicate perturbations from the mean values (turbulent contributions). The second term in the integrand is the so called "Webb-Pearman-Leuning" correction (Webb et al., 1980) which can be estimated with reasonable accuracy from the sensible (convective) heat flux density.

Conventionally, most micrometeorological estimates of exchange fluxes, such as ET, have been made over relative uniform terrain and vegetation over extensive regions, which allows simplification of the energy and mass budget equations to the vertical eddy-covariance of energy or mass, because all of the other terms are close to zero:

In this school, followed by most micrometeorologists, one rotates the coordinate system of an anemometer and forces the mean vertical velocity ω to zero to eliminate the mean flux term. However, exchange from a riparian system could not be estimated so simply, because the vegetation was not extensive nor was it uniform.

Key findings

During the measurement period (2004-2005) at the Accidental Forest the Cottonwood (Populus fremontii) dominated forest appeared to always have free access to ground water, although its ability to photosynthesize may have been affected adversely by persitant late season flooding. Net daily evapotranspiration rates in milimeters are below.

At the Deer Creek Costello site evapotranspiration rates were higher for the stand of willows we measured, but in general much less of the riparian area is covered with trees. During the summer, when the potential for evapotranspiration is highest, much of the area is covered with dead grasses. As a result the net evapotranspiration including the grass and the trees at the Deer Creek Costello site is much lower than the evapotranspiration rates measured at the Accidental Forest. Unlike the Accidental Forest the vegetation we monitored at Deer Creek experienced water stress during the measurement period. This is due to the fact that in this area the trees use water from perched aquifers during the summer, and these aquifers can dry up seasonally depending upon the timing and the strength of rainy season recharge. See Niswonger et al. (in review) for a more in depth analysis of hydrologic support of evapotranspiration at this site.

Recommendations for management & monitoring

Evapotranspiration from narrow strips of vegetation can be monitored using a method we developed in this project.

Eddy-covariance can be used for evapotranspiration measurements over more extensive regions of vegetation than narrow riparian strips.


  • Niswonger, Fogg, Kochendorfer, Paw U, Dahan, and Stewman (in review) Support of phreatophyte vegetation by heterogeneous-alluvial deposits in a water-stressed environment (Water Resources Research)


4. Aquatic-Terrestrial

Linking Aquatic and Terrestrial Systems

Ted Grosholz
Anke Müller-Solger
Erika Gallo

Preface of study task intent

The overall goal of Task 3 is to understand how the flood cycle influences the controls of primary and secondary production and how and to what degree this aquatic production supports consumers in riparian habitats. (Please also see the summary document of insect and bat trophic interactions.)

General background on study system

Primary production on inundated floodplains includes phytoplankton (free-floating algae), periphyton (attached algae), and macrophytes. In river and lake systems, both phytoplankton and attached algae, more edible, fast growing taxa predominate early in succession for both phytoplankton and attached algae and are replaced over time by less edible taxa. Algal succession toward less edible taxa may be accelerated in more productive environments with higher nutrient fluxes or irradiation. Based on observations in other systems, we predict that high nutrients and long residence times of floodplain water will promote phytoplankton or floating macrophytes. Long residence times with lower nutrient inputs will favor rooted macrophytes. Shorter residence times will favor attached algae as chief sources of local primary productivity.

Aquatic herbivore-detritivore grazers are essential links in food webs that govern the amount of algal production that is converted to terrestrial consumers. In floodplain ecosystems, we expect these assemblages to be dominated by rapidly colonizing, fast growing populations of insects and zooplankton. It is not obvious which group should dominate at various times after spillover, or under regimes with short water residence on floodplains. Because grazer abundances may be strongly affected by predation, floodplain features (rooted or floating vegetation) that provide refuges for invertebrates can have major effects on their dynamics. During a spring 2000 flood observed on the Cosumnes, chironomids initially colonized following spillover, but within weeks were replaced, first by cladocerans then copepods, whose densities then fell as larval fish increased.

Operational hypotheses

  1. Detrital inputs, rates of primary and secondary production and predation in aquatic food webs vary among different riparian and floodplain habitat types.
  2. Timing and duration of inundation influence algal community development
  3. Algal assemblages shift from edible to less edible over the course of succession
  4. Floodplain and riparian forest vegetative structure influence residence time, light, nutrient availability, and corresponding algal edibility
  5. Timing and duration of inundation, floodplain and riparian forest geomorphology and vegetative structure, and season and temperature regimes influence secondary production
  6. Aquatic insects and crustacean zooplankton both contribute significantly to secondary production
  7. Zooplankton and benthic insects differentially support native and non-native fish

Brief methods

We collected, quantified, and identified taxa in samples of zooplankton, benthic insects, periphyton, phytoplankton, and macrophytes in various sites that varied in residence time at key points in the flood cycle. We also measured stable isotopes, essential fatty acids and elemental nutrient ratios in phytoplankton, periphyton, macrophyte, and plant detritus samples as indicators of their food quality for consumers following published methods. We will experimentally measured grazing impacts and investigate zooplankton and insect growth on algae diets to infer edibility. We also conducted feeding trials to detect differences in growth and reproduction rates of invertebrates on various diets.

Key findings

Based on our preliminary data, small algal cells (especially cyanobacteria and small flagellates) dominate the phytoplankton community in the Cosumnes floodplain during flood events. During the drain period, the community tends to shift to a greater proportion of larger cells (especially diatoms). Large diatoms and cryptophytes often make up most of the phytoplankton biomass in sites with higher residence times (HRT), while smaller-celled chrysophytes often contribute a large amount of biomass at sites with shorter residence times (SRT). Ciliated protozoa are also often numerous at SRT sites.

Algal community development and “edibility” is driven both by abiotic factors such as flood phase and water residence time and by biotic factors such as trophic cascades. For example, nutritionally less valuable cyanobacteria and other very small algal cells often dominate during the initial phases of a flood event, but are soon replaced by slower growing, more edible algae, which provide food for and are eventually suppressed by rapidly expanding invertebrate populations. During the drain period, sites with lower residence time and better connectivity may be more favorable to fish which suppress the invertebrate community and allow algae of greater edibility such as smaller-celled diatoms, cryptophytes, and chrysophytes as well as many protists such as ciliates to persist. In contrast, sites with higher residence time and less connectivity may have fewer fish and more invertebrates, giving rise to a phytoplankton community dominated by larger and less edible algae such as large pennate diatoms.

Zooplankton biomass was always higher at HRT sites relative to LRT sites on the floodplain or river sites. Densities typically declined with dilution following flood events. Zooplankton biomass generally reached a maximum between 2 and 3 weeks after onset of ponding. This pattern was maintained throughout the year despite the increasing presence of fish predators from April until early June. Residence time has a significant influence on zooplankton biomass with greater initial biomass in areas of HRT. There were higher abundances of cyclopoid copepods at LRT sites and higher abundances of larger species such as Daphnia as well as a higher abundance of calanoid copepods. Fish predators were less abundant in HRT sites. Fatty acid analysis showed Daphnia has highest ALA and EPA, calanoids has high EPA and cyclopoids had high DPA. This suggests cyclopoids may be more dependent on microbial prey. Benthic insects become relatively more diverse and more abundant beginning in late February. Benthic insects were more abundant in HRT sites, and recovered more quickly at these sites with the onset of ponding.

Recommendations for management and monitoring

  1. Maintain diversity of floodplain habitats including open floodplain areas without large woody vegetation, forested floodplain and pond habitats (that become seasonally dry)
  2. Manage floodplains to ensure that multiple, repeated inundation events occur with a 2-3 period from at least early January through early May
  3. Monitoring of benthic insects and macrozooplankton should occur weekly at multiple sites on floodplain and in adjacent river channel
  4. This should also include monitoring of phytoplankton, microbial populations and microzooplankton (rotifers, ciliates) on a daily period immediately following floods and then twice weekly through the flood cycle at multiple sites on floodplain and in adjacent river channel
  5. Avoid creation of extensive HRT without periodic flood connection


5. Bird Populations

Bird Populations as Indicators of Ecosystem Health


Riparian habitat in California is one of the most productive and valuable habitats for all forms of wildlife. Yet this is also one of the most threatened habitats, with only about 5% of the state’s original riparian habitat remaining. In addition to habitat loss, California’s remaining riparian and floodplain ecosystems have been greatly altered and impaired since the mid-19th century. Historically, winter and springtime flooding provided for extensive flooded plains that were used by native fishes. Such flooding is key to the maintenance of riparian forests, once the predominant floodplain vegetation in the Sacramento Valley. Currently on most rivers, however, the natural hydrologic regime has been altered by dams and levees that alter the timing and magnitude of flows. Changes in hydrological regime and loss of habitat have had severe consequences for birds that depend on riparian habitat.

The Cosumnes River Preserve and adjoining habitat provide an opportunity to study the ecological processes necessary to restore and maintain riparian habitat through semi-passive means: specifically, levee breaching and levee setbacks that will allow natural processes to proceed. Our study focuses on evaluating the condition of the ecosystem, reflected in both recently restored habitat (through semi-passive, natural processes and through planting) and in the remaining, remnant riparian forest and scrub, using birds as a study system. Our objectives with regard to bird studies are four-fold:

  1. to evaluate current conditions of bird communities and determine whether the current habitat (remnant and restored) is able to support stable or growing populations of riparian birds
  2. to gain insight into ecological processes (biotic and abiotic) that will maintain stable or growing populations as well as a diverse bird community
  3. to develop metrics of restoration success that can inform management practice
  4. to provide the foundation for a long-term monitoring program for riparian-dependent birds and wildlife.

In 1995, in cooperation with The Nature Conservancy (TNC), PRBO began evaluating and monitoring the riparian bird communities within the Cosumnes River Preserve. PRBO implemented a multitiered integrated monitoring program following nationally standardized protocols (Ralph et al. 1993). To assess the condition of the songbird community we collected information on habitat usage, species diversity and demographic parameters (e.g., reproductive success, Howell et al. 2006). Eleven years of data compilation on bird populations have been completed as of 2005.

In 2002, PRBO began to work with partners at UC Davis and UC Berkeley in the CALFED-funded study, The influence of flood regimes, vegetative and geomorphic structures on the links between aquatic and terrestrial systems: Applications to CALFED restoration and watershed monitoring strategies. With funding from the California Bay-Delta Authority, PRBO studied riparian bird populations during 2002-2005, with the aim of evaluating conditions of bird populations, improving our ability to evaluate restoration success, and, specifically elucidating the linkages between the terrestrial bird species and the aquatic ecosystem, which is characterized by intermittent flooding during winter and spring.

Operational Hypotheses and Objectives

In this study, we evaluate the following general hypotheses:

  • Bird population and community characteristics vary in space, at least partly due to restoration state (as reflected in age or type of restoration).
  • Bird population characteristics vary in time (over the duration of the 11-year study), partly due to hydrological conditions varying over time, but also due to other factors, including climate and weather variables.
  • Observed population parameters will reflect an interaction of space and time mediated by restoration state.

We also evaluate several more specific hypotheses:

  • Remnant riparian habitat is not of sufficient quality (due to habitat degradation, habitat fragmentation, incursion of non-native flora and fauna, and other influences) in order to maintain stable populations of riparian birds.
  • Restored habitat provides habitat that improves the condition of riparian bird populations, as reflected in population trends.
  • Population trends and demographic rates will differ among sites due to restoration state.
  • Time since restoration was initiated influences characteristics of bird populations and/or the avian community.
  • Populations of riparian birds respond, directly or indirectly, to hydrological regimes (such as flooding) and/or weather variables (such as rainfall).
  • The response to hydrological state reflects the food-web mediated linkage between aquatic and terrestrial ecosystems.

To evaluate these hypotheses, we analyzed abundance data at 12 study sites over an 11-year period for 22 bird species that use riparian habitat for breeding and analyzed reproductive success for one species, the Song Sparrow, at six study sites over the same 11-year period.

Restoration, Research and Management Recommendations

We provide restoration and management recommendations based on our results from 11 years of monitoring on the Cosumnes River as well as from other PRBO riparian studies from the Central Valley. Our results support many of the recommendations provided by the California Partners in Flight Riparian Bird Conservation Plan (RHJV 2004) where more detailed recommendations for are available (

Increase floodplain connectivity and maximize winter flooding

Several of the Cosumnes focal species (Common Yellowthroat, Song Sparrow and Blue Grosbeak) prefer to nest in early successional habitat with dense understory cover. Early successional riparian habitat is dependent on floodplain connectivity and seasonal flooding which includes scouring, soil deposition and point bar formation. Results from the Cosumnes study show a positive correlation between Tree Swallow abundance during the breeding season and the number of winter flood days. In addition, Song Sparrow nest success in restored areas was also positively correlated with the number of winter flood days.

Manage for a mosaic of riparian habitat in different seral stages.

The importance of early successional riparian habitat cannot be overstated. The goals of conservation actions are often to re-create mature gallery forest. However, many bird species (Lazuli Bunting, Song Sparrow, Common Yellowthroat, Blue Grosbeak, Least Bell’s Vireo and others) either occur in low numbers or are absent in mature gallery forests. These species depend on early successional riparian habitat and are negatively correlated with characteristics associated with mature riparian (e.g., high canopy cover). We recommend managing for a mosaic of early, mid, and late successional habitat to benefit the full complement of riparian bird species.

Increase tree species richness

Planting or managing for high tree species diversity, especially large trees, will benefit many different bird species. Results from another songbird study in the San Joaquin Valley (Wood 2005) show that Bushtit and Western Scrub-Jay are positively correlated with tree species richness and studies from other sites (Nur et al. 2005) show a similar relationship with tree species richness and/or tree size (exemplified by House Wren and Tree Swallow, the latter a Neotropical migrant).

Increase understory plant volume and diversity

We recommend managing for understory growth particularly of herbaceous plants. This has been shown to be important to riparian birds in other studies (Holmes et al. 1999, DiGaudio 2001, Wood 2005, Nur et al. 2005). Mowing and spraying for weed control (e.g., Himalayan blackberry, Rubus discolor) at a site will necessarily reduce understory volume. The decision to mow should be carefully considered as a compromise between the need for weed control to promote a well-developed native understory over the long-term and the need to provide vegetative cover for ground-nesting birds during the important early successional stage of a restoration area.

Nest predator studies

We recommend studies of nest predators to better understand this threat and how it may be mediated by flooding and weather variables. Such studies will allow specific management actions to be formulated and evaluated that can mitigate predation rates. Recommended studies include continued nest monitoring using cameras to identify nest predators and quantify predation rates and Brown-headed cowbird activity at focal species’ nests. We also recommend analysis of nest survival and predation rates for all study species, especially for species that are currently declining in mature habitat. In addition, studies are needed to characterize predation risk (and the timing of predation) in relation to vegetation at or near the nest, as well as proximity of the nest to habitat edges (upland and river). A preliminary nest camera study at the Cosumnes River Preserve identified Brown-headed Cowbirds and black rats (Rattus rattus) as important nest predators (J. Hammond In prep.). Of 19 Song Sparrow nests monitored using cameras, 10 were depredated (6 by black rat [R. rattus] and 4 by Brownheaded Cowbird).


6. Data Management


In this thematic area of CRG Phase 2, we focused on three primary areas for data management: mapping, data integration, and digital repositories for long-term ecosystem monitoring.


CalJep is a spatially enabled database that reconciles or cross-walks the two prominent electronic plant distribution lists for California: CalFlora and Jepson. We intersected the distribution information from the two data sources to create a refined spatial distribution repository that can be used to examine patterns of plant diversity, distribution ranges of individual plant species or infrataxa, or vegetation associations. These data will allow scientists and resource managers to examine potential range maps for non-native plants, create range maps for plant species of restoration interest, and corroborate lines of evidence for determining appropriate management and conservation activities. We present here a detailed description of the methods used to create the CalJep geodatabase, data rendered from its creation, and a discussion of its applicability to a wide range of biogeographical and ecological questions, including restoration planning and adaptive management for the Bay-Delta ecosystem. CalJep records 7,887 plant species, subspecies, and varieties mapped onto 228 ecological subunits with corresponding distributional information for vascular plant species at varying levels of confidence. Information derived from this geodatabase is inherently as accurate as the digital floras used to create it; hence, its utility is best realized when implemented at the regional or statewide scale. CalJep provides a previously unavailable service to vegetation science in California and to resource managers operating within the Bay-Delta ecosystem.


By combining the advantages of a geographic information system for mapping and data storage with the advantages of a relational database for data management, a geodatabase offers the potential to store monitoring data in a format which is visibly and organizationally accessible. We have developed a ESRI ArcGIS 9 versioned geodatabase designed specifically to track population dynamics of vegetation patches over time.

Use of standardized data storage methods is fundamental good science, and provides the basis for incremental experimentation over the long term. Thus, we advovate for standardized framework methodologies within a geodatabase to provide a measure of certainty in future research. Our approach was to provide the opportunity to examine environmental conditions at the scale of hectares to square kilometers, and landscape parameterization at the watershed scale.

Data Management Strategies

The Cosumnes Research Group II (CRG) has employed open standards and used open source software as part of an overall data management strategy and in the process has created a data storage framework that can serve as the basis for future data transactions. We feel this has been an important data architecture decision from the inception of CRG.

We constructed this website using the Drupal Content Management System, initially integrated with the Coppermine Photo Gallery, although that gallery has been removed. In addition, the database, webserver, operating system, and programming language running this website have an Open Source software license.


The following documents are available for more detailed information on the results of our efforts, including links to data stores:

7. Floodplain Monitoring


Chinook Salmon

We reared juvenile Chinook salmon for two consecutive flood seasons within various habitats of the Cosumnes River and its floodplain (California) to compare growth rates of in river and newly created floodplain habitats. Fish were placed in enclosures in several different habitat types on the floodplain and in the river during times when wild salmon would naturally be rearing in floodplain habitats. We found significant differences in growth rates between salmon rearing in floodplain and river sites. Salmon reared in seasonally inundated habitats with annual terrestrial vegetation showed higher growth rates than those reared in a perennial pond on the floodplain. Growth of fish in the river upstream of the floodplain varied with flow and turbidity in the river. When flows and turbidity were high, there was little growth and high mortality, but when the flows were low and clear, the fish grew rapidly. Fish in tidal river habitat below the floodplain in showed very poor growth rates. Overall, ephemeral floodplain habitats supported higher growth rates for juvenile Chinook salmon than more permanent habitats in either the floodplain or river.

Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river, Jeffres, C.A.

Native and Alien Fishes

Fishes were sampled on the restored floodplain of the Cosumnes River in Central California for seven years (1998-2002. 2004-2005) during the winter-spring flooding season. 33 species of fish were captured in the flood waters, the river, and an intersecting slough. 18 species were present all years in all three habitats. The fishes fell into five groups according to how they used the floodplain: (1) floodplain spawners, (2) river spawners, (3) floodplain foragers, (4) floodplain pond fishes, and (5) inadvertent users. Eight of the abundant species were natives, while the rest were aliens. There was a consistent pattern of floodplain use, although it was modified annually by the timing and extent of flooding. The first fish to appear on the floodplain were floodplain foragers, inadvertent users, and juvenile Chinook salmon (river spawners). The next fish to appear were adult floodplain spawners, principally Sacramento splittail and common carp, although small numbers of foragers and inadvertent users from were also present. Juvenile splittail and common carp quickly grew large enough to dominate floodplain fish samples, along with juvenile Sacramento sucker and pikeminnow (river spawners).

Patterns in the use of a restored Califoria floodplain by native and alien fishes, Moyle, P.B., Crain, P.K., Witener, K.


CRG2 Reports and Publications


  Name and Description File size
PDF A Spatial Distribution Database of CalFlora and Jepson Plant Species
A Spatial Distribution Database of CalFlora and Jepson Plant Species, San Francisco Estuary and Watershed Science, Viers, J.H., Thorne, J.H., Quinn, J.F.
Viers, J.H.
15.83 MB
PDF Ahearn, D.S., Sheibley, R.W., Dahlgren, R.A., Keller, K.E. Temporal dynamics of stream water chemistry in the last free-flowing river
Temporal dynamics of stream water chemistry in the last free-flowing river draining the western Sierra Nevada, California
Dylan S. Ahearn, Sheibley, R.W., Dahlgren, R.A., Keller, K.E.
1.02 MB
PDF Ahearn, Dylan S., Viers, Joshua H., Mount, Jeffrey F., Dahlgren, Randy A., 2006. Priming the productivity pump: flood pulse driven trends in suspended algal biomass distribution across a restored floodplain
Ahearn, Dylan S., Viers, Joshua H., Mount, Jeffrey F., Dahlgren, Randy A., 2006. Priming the productivity pump: food pulse driven trends in suspended algal biomass distribution across a restored foodplain by
Ahearn, D.A., Viers, J.H., Mount, J.F., Dahlgren, R.A.
0.79 MB
PDF Booth, E.G., Mouth, J.F., Viers, J.H., Hydrologic Variability of the Cosumnes River Floodplain, San Francisco Estuary & Watershed Science (2006)
Booth, E.G., Mouth, J.F., Viers, J.H., Hydrologic Variability of the Cosumnes River Floodplain, San Francisco Estuary & Watershed Science (2006)
Booth, E.B., Viers, JH, Mount J.
0.76 MB
PDF Crain, P.K., Whittener, K., Moyle, P.B. Use of a Restored Central California Floodplain by Larvae of Native and Alien Fishes, American Fisheries Society Symposium 39:125-1
Use of a Restored Central California Floodplain by Larvae of Native and Alien Fishes
Crain, P.K., Whitener, K., Moyle, P.B.
0.62 MB
PDF Florsheim, J.L., Mount, J.F. Changes in lowland floodplain sedimentation processes: pre-disturbance to post-rehabilitation, Cosumnes River, CA, Geomorphology 56 (2003) 305?323.
Changes in lowland floodplain sedimentation processes: pre-disturbance to post-rehabilitation, Cosumnes River, CA
Florsheim, J.L., Mount, J.F.
1.11 MB
PDF Florsheim, J.L., Mount, J.F. Restoration of floodplain topography by sand-splay complex formation in response to intentional levee breaches, Lower Cosumnes River, California, Geomorphology 44 (2002) 67-94.
Restoration of floodplain topography by sand-splay complex formation in response to intentional levee breaches, Lower Cosumnes River, California
Florsheim, J.L., Mount, J.F.
1.41 MB
PDF Moyle, P.B., Crain, P.K., Whitener, K. d, Patrick K., Mount, J.F. Alien fishes in natural streams: fish distribution, asse
Alien fishes in natural streams: fish distribution, assemblage structure, and conservation in the Cosumnes River, California, U.S.A.
Moyle, P.B., Crain, P.K., Whitener, K. d, Patrick K., Mount, J.F.
0.18 MB
PDF Mueller-Solger, A.B., Jassby, A.D., Mueller-Navarra, D.C. Nutritional quality of food resources for zooplankton (Daphnia) in a tidal freshwater system (Sacramento?San Joaquin River Delta), Limnol. Oceanogr. 47(5), 2002, 1468-1476.
Nutritional quality of food resources for zooplankton (Daphnia) in a tidal freshwater system (Sacramento?San Joaquin River Delta)
Anke B. Mueller-Solger, Jassby, A.D., Mueller-Navarra, D.C.
0.16 MB
PDF Viers, J.H., Hogle, I.B., DiPietro, D., Arora, S., Gubaydullin, M., Quinn, J.F., Geodatabase Application for Invasive Plant Tracking and Coordinated Habitat Restoration
Geodatabase Application for Invasive Plant Tracking and Coordinated Habitat Restoration
Viers, J.H., Hogle, I.B., DiPietro, D., Arora, S., Gubaydullin, M., Quinn, J.F.
0.44 MB

Quarterly Reports

  Name and Description File size
PDF CRG Quarterly Report, 2002 Q IV
Cosumnes Research Group, CalFed Quarterly Report, Fourth Quarter, 2002
1.18 MB
PDF CRG Quarterly Report, 2003 Q I
Cosumnes Research Group, CalFed Quarterly Report, First Quarter 2003
0.54 MB
PDF CRG Quarterly Report, 2003 Q II
Cosumnes Research Group, CalFed Quarterly Report, Second Quarter 2003
2.19 MB
PDF CRG Quarterly Report, 2003 Q III
Cosumnes Research Group, CalFed Quarterly Report, Third Quarter 2003
0.21 MB
PDF CRG Quarterly Report, 2004 Q I
Cosumnes Research Group, CalFed Quarterly Report, First Quarter 2004
0.17 MB
PDF CRG Quarterly Report, 2004 Q II
Cosumnes Research Group, CalFed Quarterly Report, Second Quarter 2004
0.04 MB
PDF CRG Quarterly Report, 2004 Q III
Cosumnes Research Group, CalFed Quarterly Report, Third Quarter 2004
0.07 MB
PDF CRG Quarterly Report, 2004 Q IV
Cosumnes Research Group, CalFed Quarterly Reports, Fourth Quarter, 2004
0.24 MB
PDF CRG Quarterly Report, 2005 Q I
Cosumnes Research Group, CalFed Quarterly Report, First Quarter 2005
0.55 MB
PDF CRG Quarterly Report, 2005 Q II
Cosumnes Research Group, CalFed Quarterly Report, Second Quarter 2005
0.3 MB
PDF CRG Quarterly Report, 2005 Q III
Cosumnes Research Group, CalFed Quarterly Report, Third Quarter 2005
0.05 MB

Archived Reports

  Name and Description File size
PDF Amphibian Species of the Cosumnes River Watershed
Amphibian Species of the Cosumnes River Watershed
0.02 MB
PDF Biomicrometeorological Measurement of Riparian Vegetation Evapotranspiration
Biomicrometeorological Measurement of Riparian Vegetation Evapotranspiration
John Kochendorfer, Kyaw Tha Paw U
0.12 MB
PDF Bird Species of the Cosumnes River Watershed
Bird Species of the Cosumnes River Watershed
0.25 MB
PDF Evaluation of Fisheries Relating to Floodplain Restoration on the Cosumnes River
Evaluation of Fisheries Relating to Floodplain Restoration on the Cosumnes River Preserve.
0.04 MB
PDF Fish Species of the Cosumnes River Watershed
Fish Species of the Cosumnes River Watershed
0.03 MB
PDF Mammal Species of the Cosumnes River Watershed
Mammal Species of the Cosumnes River Watershed
0.06 MB
PDF Options for conjuntive water management to restore fall flows in the Cosumnes River basin, California
Options for conjuntive water management to restore fall flows in the Cosumnes River basin, California
Jan Fleckenstein
0.36 MB
PDF Plant Species of the Cosumnes River Watershed
Plant Species of the Cosumnes River Watershed
0.11 MB
PDF Reptile Species of the Cosumnes River Watershed
Reptile Species of the Cosumnes River Watershed
0.03 MB