The present study aims at assessing changes in macroinvertebrate metrics in relation to the effects of agricultural land use in a lowland river. Cluster analysis techniques were applied to group river sites according to the similarity of total and relative abundances of taxonomic groups. Riverbed morphology and riparian vegetation were the main environmental variables differentiating between clusters. The total abundance of macroinvertebrates, and absolute and relative abundances of EPT, Coleoptera, and Trichoptera were significantly higher in the river sites with a narrow belt of riparian forest in comparison with groups of deforested and straightened river sites. Macroinvertebrate community status based on biotic indices was significantly higher in the natural forested river reaches and was classified as good or even very good, whereas the status of most of the rest of the sites was recognized to be moderate or poor. None of macroinvertebrate variables correlated with water quality parameters. The presence of forest belts along riversides seems to support the good status of macroinvertebrate communities, even if concentrations of nitrogen and phosphorus in the river are elevated due to agricultural runoff and exceed maximum permissible concentrations valid in Lithuania. However, single macroinvertebrate metrics, differently from integral metrics, indicated alterations in water quality of the studied river.