Most publications on the influence of environmental factors on macroinvertebrate communities focus on large rivers, whereas relatively few examine small watercourses in agricultural areas, which, due to their size and pressure from intensive agricultural production, are much more susceptible to the effects of unfavourable environmental conditions or anthropopressure. The aim of our study was to compare the biodiversity of macrozoobenthos assemblages and to determine the effects of physicochemical and hydrological conditions on their abundance and density in 10 small rivers in agricultural areas located in northwest (53°23′ N 15°14′ E) and central (52°11′ N 20°48′ E) Poland. In total, 105 taxa were recorded, with the majority being euryoecious. Among the assessed physicochemical parameters, oxygenation was found to affect the density and number of taxa; another important factor was the content of nitrate nitrogen. Sensitivity to changes in water temperature was observed in some macrozoobenthos taxa (especially Decapoda). Of the examined hydrological parameters, the greatest effects were exerted by speed, flow, and depth.