In the past a rich side arms floodplain network with high biodiversity developed in the Danube River section downstream of Bratislava. In consequence of the Gabčíkovo river barrage system construction one part of side arms was flooded by the Hrušov reservoir, an other, smaller part dried up. Several, formerly almost terrestrial zed side arms on the both banks of the new reservoir were restored due to ground water level increase. Major portion of the side arms area in the Slovak part of the floodplain (situated between river kilometers 1840 and 1820) is supplied by water from the head-race canal of the power plant. Prior to damming, in the parapotamon-type side arms (sense Roux et al., 1982) a strong development of zooplankton occurred in the warm season of the year. After damming zooplankton abundance and biomass dropped and tychoplanktonic (benthic and littoral) species became predominant. This was caused by disruption of former connectivity of side arms with the main channel and by substitution of former fluviatile-stagnant regime by permanently fluviatile one. Euplanktonic species continue to dominate in the medial zone of the plesiopotamon-type side arms; however, littoral forms increasingly penetrate into it. Also the latter fact is caused by loss of arms interconnection with the main channel and by accelerated terrestrialization process. The authors recommend taking measures, which could provide conditions nearer to the natural ones.