The fish diversity of the Slovak segment of the Danube (representing the transitional zone from the rhithron to the potamon) was under the control of the inland delta which existed in this region until 1992. Seventy-six species were recorded in the studied river section: 61 species were native, 11 were exotic, 5 or 7 were invaders from the lower sections of the Danube, 3 species (and one form) became extinct, and 7 species were not detected during the past 20 years. The increasing pollution until 1985 decreased the fish species richness, but the improvement of water quality thereafter rose their number. However, the construction of the Gabcíkovo River Barrage System put in operation in October 1992 started to change substantially fish species richness and quantity, and fish catch. The formerly functional inland delta controlled by the pulsating discharge disappeared, and was changed to an artificial system of isolated or only marginally connected habitats. The upstream fish migration was stopped by the Gabcíkovo dam and weirs in Cunovo. Therefore, the fish fauna of the side arms lost contact with fish of the main channel and of the bypass canal downstream. The loss of spawning habitats had fatal effects, especially for the wild carp and the pike, which number rapidly decreased. In general, the number of fish species, their density, and fish catch decreased significantly. To improve the situation, it is proposed: 1) to restore the bilateral connection between the main channel and the side arms, 2) to ensure fish migration between the main channel and the side arms, and 3) to simulate the original flooding of the floodplain.