Investigating forces driving the structure of aquatic communities has long been an important issue in ecology. In the present study, we focused on the effects of changed water supply for aquaculture ponds on phytoplankton, zooplankton and macrozoobenthos communities during two seasons of rearing common carp. We compared these communities between two types of inflow water: surface sources of water – a reservoir pond, two open wells and a small stream and groundwater – deep tube well. Significant changes were observed in environmental variables after the introduction of the groundwater source: oxygen concentration and water hardness decreased, while conductivity, phosphorus and un-ionized ammonia increased. Results revealed that all investigated groups, except Mollusca (macrozoobenthos), decreased in species richness, abundance and biomass due to changed water chemistry, but differed in the level of susceptibility. Rotifera and Cladocera were the most affected showing a sharp decline in density and number of species since 66% of species disappeared from the ponds. The abundance of Copepoda was relatively high although significantly lower under new conditions, with adults being more tolerant to changed inflow water than nauplii larvae. Phytoplankton had the highest potential to replace previous species with newcomers more adapted to changed water chemistry, providing 36 immigrant species, whereas 49 became extinct. Although mainly influenced by fish predation, Chironomidae (macrozoobenthos) were undoubtedly affected by changed water chemistry. These results suggest profound changes in three key ecological groups produced by significant changes of important environmental variables and water quality after the shift from surface to groundwater supply.