The aim of the study was to determine changes in potamoplankton structure caused by lakes in the fluvial system of the small River Wel. The river flows through 10 lakes. The study was conducted in 2007 and 2008. The selection of sites enabled the assessment of the impact exerted by hydrological conditions of the river on zooplankton, as well as the determination of the effect of lakes situated within the river course on the analysed assemblage of organisms. In total 95 species were determined with an average abundance 1026 ind. 10 dm-3. Rotifers dominated qualitatively and quantitatively and among crustaceans - Copepods. Lakes seem to be the main source of zooplankton in the fluvial system of the Wel River. The lakes disturb the river continuum, but their impact on the structure of zooplankton is short-lived. Due to the presence of flow-through lakes along the river, species richness of zooplankton in the Wel River is similar to that in large rivers.