We sampled freshwater suspended particulate organic matter (POM) to determine its carbon and nitrogen stable isotope composition and collected co-located water chemistry data in California's Sacramento—San Joaquin Delta from sites on the Mokelumne and Cosumnes rivers. A 10-km2 area was sampled across 12 sites and divided among three habitat types (i.e. riverine, slackwater/slough, and off-channel), 34 times between November 2016 and July 2017. Here, we describe the variability in water quality and POM variables, and assess factors associated with that variability using dimensional reduction and linear modelling within the context of our habitat types. The stable isotope composition of freshwater POM and water chemistry variables differed significantly across small areas (<10 km) and short time frames (weekly). Hydrological connectivity amongst sites was found to be an important factor in the isotopic and elemental composition of POM. During periods of low hydrological connectivity, in situ dynamics were strongly associated with differentiation of POM in different habitats. Discharge (16–433 m3/s) and water temperature (8–30°C) were the variables most associated with variations in the composition of POM. Slackwater sites showed the greatest variability in POM composition, which may be symptomatic of longer water residence times, increased cycling rates of nutrients and organic matter, or a combination of the two. Variability in POM stable isotope composition demonstrates that caution should be exercised when interpreting analyses that assume a static POM stable isotope composition based on two-end member mixing. Unconstrained variability in space or time could confound interpretations of models and data. Moving forward, conceptual and numerical models for river ecosystems that emphasise temporally heterogeneous lateral exchange amongst habitat patches should be prioritised when considering restoration efforts and monitoring outcomes.

Website: https://onlinelibrary.wiley.com/doi/abs/10.1111/fwb.13522