The diel distribution of early juvenile fish communities from two temperate freshwater reservoirs that differed in cover of submerged aquatic vegetation was investigated. In the daytime, about 99.9% of the juvenile fish community from the plant‐rich Žlutice Reservoir was found in the nearshore belt of submerged aquatic vegetation reaching an average abundance of ~7982 inds. 1000 m−3. In contrast, in the pelagic habitat, few fish were found at day. In the plant‐poor Římov Reservoir, 98.9% of juveniles occupied the pelagic habitat during daytime and reached an average abundance of ~333 inds. 1000 m−3. Vertical distribution of fish in the pelagic habitat in both water bodies was affected by steep thermal and oxygen stratification and no individuals occurred below 6 m depth. At night, 88.8% of the juvenile fish community from the plant‐rich Žlutice Reservoir was in the pelagic habitat with an average abundance of ~1423 inds. 1000 m−3. Their diel horizontal shifts were much more pronounced compared to the community from the Římov Reservoir that reached an average nighttime pelagic abundance of ~523 inds. 1000 m−3. Only 1.1% of the juvenile fish community in the Římov Reservoir was found in the littoral during the daytime and 0.7% at night reaching an average daytime abundance of ~1688 inds. 1000 m−3 and average nighttime time abundance of ~1664 inds. 1000 m−3. This study indicates that if a well‐developed littoral zone with abundant aquatic vegetation is present, early juvenile fish will perform diel horizontal movement in temperate stratified reservoirs.