Strong changes in stable isotope tracers commonly occur across estuarine salinity gradients from freshwater to the sea. The tracer gradients reflect the different geochemistries and mixing of freshwater and seawater, and these bottom-up geochemical influences are recorded in estuarine food webs in the isotopic compositions of animals. Conservative mixing calculations suggest that watershed-level inputs of freshwater and nutrients should exert strong influences on isotopic values of estuarine consumers, especially consumers such as bivalves that largely depend on phytoplankton production. Deviations from conservative isotope mixing also occur, and the magnitude of these deviations measures the strength of within-estuary organic matter cycling for estuarine food webs, especially inputs of non-phytoplankton foods such as macrophyte detritus and benthic algae. Measuring consumer isotopes across salinity gradients should be a relatively simple way to monitor effects of watershed nutrient loading and hydrologic flushing in supporting estuarine fisheries production.