Fish larvae play an important structuring role for their prey and show ontogenetic shifts in diet. Changes in diet differ between species and habitats and may also be affected by turbidity (eutrophication). We investigated the diet (stomach content) and the food selection (ratio of ingested prey and prey availability) of roach and perch larvae in a clear lake and of roach, perch and pikeperch larvae in a turbid lake multiple times during spring to autumn. The diet of the fish larvae changed with size, and for roach and perch larvae between the lakes. Coexisting species of fish larvae had different diets in the two lakes, pointing to resource partitioning; yet, in the clear lake, medium-sized larvae had a high diet overlap, suggesting a competitive relationship at this developmental stage. In the clear lake, roach larvae showed diel differentiation in diet, while perch demonstrated diet shifts between habitats, which probably aided in reducing competition and also evidenced an effect of light on the larval prey capture and/or predator-fish larvae interactions. In the turbid lake, roach and perch larvae did not reveal differences in diet between habitats or time of the day, owing to homogeneity of food items and poor light conditions. However, the diet of pikeperch larvae differed between day and night following daily variations in the abundance of its preferred prey. The roach larvae were highly selective for Bosmina, Daphnia and benthic cladocerans, perch larvae generally consumed what was available, while pikeperch primarily preyed on cyclopoid copepodites. We conclude that turbidity acted as a cover for fish larvae in the turbid lake. Under eutrophication-induced turbidity scenarios the effects of fish larvae on their prey are stronger (i.e., high selectivity for several resources) than that of larvae in clear waters, creating a negative feedback on the path to restore water clarity.