This study describes the influence of urban area on plant communities and benthic invertebrates inhabiting the Słupia River (northern Poland). Ten plant communities and 37 macrozoobenthos taxa were determined during four seasonal samplings at 25 sampling sites (October 2005 and January, April, and August 2006). The obtained data set was statistically evaluated in order to reveal the influence of anthropogenic transformations on the investigated communities against the background of other abiotic factors. Multivariate regression tree (MRT) method was used for vegetation, while for benthic fauna, both MRT and artificial neural network (ANN) methods were applied. The following explanatory variables were used: season, water temperature, and salinity; location of a sampling site; degree of human impact on the riverbed; microhabitat; and substrate type. MRT analyses showed significant differences in plant community structure depending on the location of a sampling site, indicating the influence of anthropogenic pressure, while macrozoobenthos composition differed significantly only between seasons. The overall ANN model proved the importance of type and location of a sampling site for the approximation of benthic fauna density. Additionally, influence of the explanatory variables on the consecutive macrozoobenthos taxa was analyzed on the basis of separate ANN.