Coastal waters are important in linking zoobenthos and fish, as many coastal fishes feed on benthic prey in these habitats. Major drivers, such as eutrophication and climate change, may alter this link, whereas shifts in the importance of these drivers may induce different responses in zoobenthos and fish, respectively, potentially changing productivity of coastal ecosystems. The aim of this study was to assess in which way abundance and distribution of benthic-feeding fish and biomass of zoobenthos have changed over time in response to eutrophication (Secchi depth) and climate change (temperature and salinity), respectively. This was done by analyzing gross changes in the responses over three decades (1983–2012) and across depth zones. Eutrophication and climate change caused different though specific impacts on fish and zoobenthos, respectively. Throughout the 1980s, increasing benthic-feeding fish abundance in shallow waters (<6 m) was primarily attributed to eutrophication (decreasing Secchi depth), implying increased system productivity. During the 2000s, the effect of eutrophication levelled out, whereas temperature caused contrasting development of fish abundance at different depth zones. Shallow waters had lower fish abundances during warm years compared with colder ones, while the abundance increased in deeper, aphotic waters (6–20 m). In the deep waters, zoobenthos showed a contrasting, declining trend in biomass, coinciding with the decrease in salinity during the 2000s. This suggests altered ecosystem productivity and potential food shortage for benthic-feeding fish exploring the deep waters. An intensification of these trends is likely in the future, as climate change scenarios suggest further temperature increase and salinity decrease.