The aim of the study was to demonstrate the relationship between macroinvertebrate assemblages and aquatic vegetation interacting with chemical and geomorphological factors. The survey was carried out in the catchment of a lowland river in Poland in the year 2009. Macroinvertebrate samples were collected on 19 river sites during two campaigns (spring and autumn) and 13 macroinvertebrate metrics were calculated. Indices were selected to reflect pressures associated with organic pollutants, morphological and general degradation of rivers. Hydromorphological assessment was undertaken according to the River Habitat Survey (RHS). Water samples for chemical analysis were collected monthly during the whole year, and nine chemical parameters were analysed. Macrophyte surveys made it possible to calculate seven parameters. It was found that macroinvertebrates collected in spring and autumn showed very different patterns and that only the spring samples showed a significant relationship between macroinvertbrates and water quality, which means that spring sampling is most important for biomonitoring. Only three macroinvertebrate metrics, i.e. SIGI (German Saprobic Index), EPT (indicating the relative abundance of Ephemeroptera, Plecoptera and Trichoptera) and MBI (index used for river ecological status assessment), responded significantly to water pollution. Macrophytes and macroinvertebrates responded differently to environmental gradients and these organism groups deliver different information for monitoring.