My laboratory group has been studying the ecology and conservation of freshwater and estuarine fishes in California for over 40 years. We have documented the status of all native freshwater fish species in California throughout this period, with special interest in salmon and other anadromous fishes. The interactions among native and alien species in environments with varying degrees of disturbance have provided a major basis for our ecological studies and have lead to management actions to improve conservation of native fishes. In recent years, we have developed large data sets on the status, distribution, and ecology of native and alien fishes of California, and have quantified potential impacts of climate change on each species. The team has also created data bases on California dams and their impacts on fishes, especially through altered flows. These data sets are a major source of publications. Another research focus is the ecology and conservation of fishes of the San Francisco Estuary, research that includes 35 years of monthly fish and macroinvertebrate sampling at multiple locations in Suisun Marsh. Current research has extended the Suisun Marsh sampling to the North Delta. We are especially interested in the impact of the current drought on both estuarine and freshwater fishes of California and on the impacts of new water management schemes on native fishes and on ‘restoration’ efforts for them. Increasingly, we talk about our research results in the context of novel ecosystems and reconciliation ecology. A good example of this is our work on the Yolo Bypass and other floodplain systems, where management for desirable species has to be imbedded in highly altered systems containing many alien species and often seemingly conflicting land uses.