The phytoplankton structure of the Vilejka fish farm ponds and watercourses which are its water sources and water intakes — the Vilia and the Smerdia rivers was studied. It was determined that the phytoplankton development level in the large Vilia River is comparable to the development level in fish farm ponds exposed to targeted trophic increase. The fundamental difference in the taxonomic phytoplankton structure between all studied ecosystems was noted. A significant impact of the farm on the small Smerdia river phytoplankton in some years during the water discharge from the pond was determined. The fundamental difference in the taxonomic phytoplankton structure    in the Vilia River and Smerdia River evidences the fact that phytoplankton of the Smerdia River, which is the Vilia River tributary, has virtually no effect on the phytoplankton formation directly in Vilia. When injected into the flow, tributary phytoplankton specimen are replaced by the well-formed algoflora of the Vilia River watercourse.