Juvenile 0+ fish communities in three adjacent stretches of two lowland rivers with different degrees of habitat modification were surveyed using electrofishing and evaluated as indicators of fish assemblage reproductive success and spatial distribution. Both rivers originally meandered through large flood plains, however both have been regulated and channelised, to a varying extent, during the last century. The first study stretch, the Czech stretch of the Morava River (69.4 – 92.8 r. km), was regulated by five weirs and completely separated from its floodplain. The second and third study stretches, the Slovak stretch of the Morava River (33.5 – 69.4 r. km) and the Dyje River (0 – 26.7 r. km), were not interrupted by weirs and their floodplain areas remain connected, though partially modified. The total number of 0+ fish species in all of the stretches recorded over three years was similar (22, 23 and 25 spp. resp.). The lowest value of the Shannon index of species diversity and the highest value of total relative density (CPUE) were documented in the Czech regulated-channelised stretch. Significant differences in species richness and relative density were documented among habitats.