Our study was carried out in the middle basin of the Biebrza River (NE Poland) in the periods of June and September in 2011 and 2012. From among numerous side-arms, four objects have been selected for analyses of macrozoobenthos structure and biomass. Two lakes exhibited a lentic character due to a long-lasting isolation from the river channel, one presented a lotic, and one was of a semi-lotic character. Differentiated hydrological conditions within the study period enabled comparative studies: in 2011 appeared low and high water levels, while in 2012 no low water appeared and high water levels prevailed, which influenced the wetland conditions and inhabiting aquatic zoocenoses. During the study 352 individuals of benthic invertebrates with a total biomass of 288 g of wet weight were collected. Among the studied lakes we found the highest values of biodiversity indices in a lotic reservoir, while the highest densities and biomasses were in a semi-lotic reservoir. Nevertheless, the composition and abundance of benthic invertebrates in the studied lakes differed significantly from type-specific communities found in the floodplain lakes in other regions. A substantially lower level of macrozoobenthos diversity in floodplain lakes of the Biebrza River is indicative of less favorable conditions for macrozoobenthos development due to frequent water level fluctuations.