Anthropogenic perturbations paired with increasing climatic changes, affect the biota composition and ecosystem services provided by highly productive estuarine transitional ecosystems worldwide. To determine driving forces affecting fish stocks in an estuarine habitat, we created a periodic time series over the last four decades (1984–2022) combining fish species compositions and densities with environmental conditions along the course of the temperate mesotidal Elbe estuary. We detected major changes in the species composition alongside with changes in life cycle guilds composition. With a relative increase of marine-estuarine opportunists and reduction of diadromous species, the fish fauna of the Elbe estuary has become more similar in guild structure compared to macro tidal estuaries in Europe. Improvements in water quality in the 1990s were accompanied by increased fish densities, specially smelt (Osmerus eperlanus), until 2010. Anthropogenic hydromorphological interventions, however, could have led to an increase in suspended particular matter until 2022, which combined with reduced river runoff and poor oxygen concentrations in summer months acted as poor environmental conditions for fishes in the estuary. Mean fish densities dropped by over 91 % compared to 2010 to an all-time low in the data. This reduction was primarily a result of a decline of the key species smelt in the system along with declines of twaite shad (Alosa fallax), flounder (Platichthys flesus), ruffe (Gymnocephalus cernua), common bream (Abramis brama) and other species. On the contrary, marine species herring (Clupea harengus) and whiting (Merlangius merlangus) densities increased. Overall, the time-series provides insight into the strong impact of human intervention that are however expected to lead to further stressors.