Having analyzed fry seine catches from the lower reaches of the rivers flowing into Lake Ilmen and from floodplain lakes in the Msta and Lovat river deltas, we have updated information on the composition of the fish population of reservoirs and watercourses of the Lake Ilmen catchment. In total, 19 fish species belonging to six families were present in the catches in 2020–2021. The fish communities of the lower reaches of the rivers Volkhov, Lovat, Shelon, Veronda and floodplain lakes of the Lovat and Msta deltas featured high similarity, with the predominance of limnophilic species, in contrast to the riffle sections of the Msta, where rheophilic fish species dominated in abundance. At most survey sites, the catches were dominated by the main harvestable fish species of Lake Ilmen. The biomass of fish underyearlings in the autumn period of 2020 in floodplain lakes of the Lovat and Msta deltas was four to six times that of in the littoral zone of Lake Ilmen and comparable to the levels at survey sites in the lower reaches of the rivers Msta and Volkhov. Fry seining of river and lake areas within the Novgorod Region revealed fish species not previously reported for the Lake Ilmen catchment or formerly considered rare in the catchment. Lake Ilmen catchment being hydrologically isolated from the main invasion pathways as well as the absence of intentional acclimatization activities are factors promoting the stability of the native composition of the fish fauna and the reason why only one naturally dispersing species, the silver carp, has become naturalized in Lake Ilmen.