Rapid changes, including warming and freshening, are occurring in coastal marine ecosystems worldwide. These environmental changes have the potential to alter ecosystem energetics by influencing availability of food sources and organism physiology. We investigated the influence of oceanographic variability on food availability and quality to benthic and pelagic suspension-feeders using detailed observations of phytoplankton, particulate organic matter (POM) detritus, and diverse biomarkers (fatty acids and carbon, nitrogen, and sulfur stable isotopes) along a salinity gradient in the San Juan Archipelago, Washington, U.S.A. We tested the hypothesis that freshwater input from riverine discharge would cause significant changes to oceanographic conditions and reduce food quality (indicated by essential fatty acids; EFA), owing to greater contribution of terrestrial organic matter. Contrary to our expectations, availability of high-quality marine-derived POM increased with freshwater input (reduced salinity). Phytoplankton biomass and biomarker composition responded to oceanographic change similarly across tidal and seasonal scales. Using a meta-analysis spanning a range of spatial and temporal scales, we found that chlorophyll a, temperature, dissolved oxygen (DO) and pH were consistently and significantly higher at reduced salinity. The increase of DO and pH corresponding to higher phytoplankton biomass in low salinity water signifies an important feedback of biological activity on seawater chemistry. This analysis supports the use of salinity as an indicator of processes controlling food availability and oceanographic conditions in this region. Collectively, these results highlight the importance of ecosystem connectivity in coastal environments and produce hypotheses for expected changes related to altered river discharge dynamics.