Floodplain borrow pits created during dike construction for flood protection along regulated lowland rivers are suggested as convenient surrogate habitats for fish communities where natural floodplain features have been lost. Fish community structure and reproduction success in three borrow pits located in the channelised floodplain of the River Dyje, Czech Republic were studied over 3 years. Short-term floods supported the spawning of phytophilic and phyto-lithophilic species; batch spawners capitalised on late summer flood conditions. The highest species richness of 0+ juvenile fishes occurred at sites with extended periods of flooding, at least for 2 months. Flooded vegetation was inhabited mainly by juvenile cyprinids, while 0+ percids were distributed evenly along the littoral zone. Shoreline remained bare even during higher water levels before complete inundation because of the steep banks, and therefore fish were not able to benefit from higher water levels. Borrow pits appear to function as a substitute habitat for fish and their reproduction, but only if they are properly constructed with shallow areas providing appropriate nursing conditions for 0+ fish growth and survival.