The aim of our study was to compare the biodiversity of zooplankton in experimental ponds with various combinations of fertilizers and supplementary fish feed. Zooplankton samples were collected twice a month from April to September 2015. Rotifers were the most diverse and the most abundant zooplankton group. The most abundant rotifer species in all the ponds were Anuraeopsis fissa, Keratella cochlearis, Keratella tecta, Polyathra sp., and Trichocerca pusilla, while among cladocerans there was Bosmina longirostris. Optimal conditions for developing the Rotifera were found in the experimental ponds with standard fertilization and standard feeding of fish. The highest biomass was achieved by zooplankton in the ponds with accelerated fertilization and standard feeding of fish.