Abstract The effect of agriculture on fish assemblages was assessed using electric fishing data from 108 sites on 27 medium-sized rivers running through organic soils in central and northern Finland. The intensity of agriculture was quantified as the percentage of the catchment area used for agriculture (range 0–31%). High correlations (r2 = 0.68–0.86) were found between the intensity of agriculture and water quality parameters, especially total phosphorus, suspended solids and chemical oxygen demand. Densities of bullhead, Cottus gobio L., alpine bullhead, Cottus poecilopus Heckel, minnow, Phoxinus phoxinus (L.) and brown trout, Salmo trutta L., declined with increasing intensity of agriculture. Conversely, density of perch, Perca fluviatilis L., and roach, Rutilus rutilus (L.), increased with intensity of agriculture. A fish-based index developed for the evaluation of the ecological integrity of rivers correlated negatively with the intensity of agriculture.