This phytoplankton study was conducted from May to September 2002, 2003 and 2005 during fountain-based water aeration in the pelagial of Jeziorak Mały urban lake in Poland. Differences in the abundance and biomass of phytoplankton groups (cyanobacteria, diatoms, chlorophytes, dinoflagellates, chrysophytes and cryptomonads) related to physico-chemical water parameters were analyzed at the fountain and in the lake centre. Fountain water-mixing changed phytoplankton growth likely by decreasing water temperature, oxygenation and nutrient concentrations. These induced a disturbance in the cyanobacteria and stimulated growth of phytoplankton groups in the water column. High phytoplankton abundance at 1 m depth at the fountain could relate with phytoplankton sinking in the water column. This additional water mixing also intensified sedimented organic matter decomposition, thus enhancing nutrient uptake by phytoplankton. These results are important for future shallow urban lake management.