In this study, we analyse the qualitative and quantitative structure of benthic macroinvertebrate communities in three oxbow lakes differing in hydrological connectivity, located along the lowland Łyna River (NE Poland). The lakes differed in the extent of surface contact with the main river channel and represented lotic, semi‐lotic, and lentic types of water bodies. Mean benthofauna density ranged from 0.9 · 103 (lentic) to 2.0 · 103 indiv. m−2 (semi‐lotic) and mean biomass ranged from 16 (lentic) to 202 gww m−2 (semi‐lotic); these differences were not statistically significant (P ≤ 0.05). The diversity (Shannon's index) was highest in the lotic and lowest in the lentic ecosystem. It was predominated by Oligochaeta and Chironomidae larvae. The highest, statistically significant differences were observed between the densities of Ephemeroptera larvae (P ≤ 0.05), Megaloptera larvae (P ≤ 0.05) and Arachnida (P ≤ 0.01). In terms of biomass, gastropods prevailed in the semi‐lotic, bivalves in the lotic and Chironomidae larvae in the lentic ecosystems. Amongst gastropods, Viviparus viviparus L. dominated in oxbows connected with the river. Our results, supported by the canonical correspondence analysis (CCA) and hierarchical cluster analysis showed a significant effect of hydrological connectivity, which in a direct or indirect way influenced the macroinvertebrate structure in oxbow lakes. As shown by CCA, a free exchange of water between oxbows and the river channel promotes favourable conditions for the development of hydrobionts. Copyright © 2015 John Wiley & Sons, Ltd.