This dataset contains a time series of species-specific fish abundances and covariates for 1180 fish sites in English rivers. Sites with at least ten annual fish surveys in the Environment Agency’s (EA) National Fish Population Database (NFPD) between 1975 and 2017 inclusive were selected. Covariate data include habitat quality indicators (River Habitat Survey and HABSCORE outputs), climatic variables (Gulf Stream and North Atlantic Oscillation indices), land-use change, river hydrology, water temperature, effluent dilution factor and concentrations of chemical determinands. The work was supported by the Natural Environment Research Council (Grant NE/S000100/2). Full details about this dataset can be found at https://doi.org/10.5285/b0afb78e-a0cb-4762-9220-659211ae3a5e