There is currently a critical knowledge gap in how eutrophication and climate variables separately and interactively impact the dynamics of marine ecosystems. Based on long-term monitoring data we quantified the separate and combined impacts of nutrient loading, temperature, salinity, and wind conditions on zooplankton, zoobenthos and fish inhabiting a brackish water ecosystem in the Gulf of Riga. Changes in zoobenthos communities and herring stock were largely explained by climate variables. Zooplankton species were related to both eutrophication and climate variables, and models combining all environmental variables explained additional variation in zooplankton data compared to the separate models of climate and eutrophication. This suggests that zoobenthos communities and herring stock are largely driven by weather conditions, whereas the combined effect of weather and nutrient loads are likely the cause for dynamic zooplankton communities in the Gulf of Riga.