Spatial distribution of young-of-the-year (YOY) and older roach, rudd, perch and ruffe was compared in two artificial lakes with macrophytes present and absent, and a valley reservoir, using gillnets. Almost all species of interest and both age categories preferred benthic habitats. The depth distribution in benthic habitats was relatively consistent across water bodies with the highest fish densities found in the shallowest depths. In the macrophyte-rich lake, YOY roach and perch utilize the 3–6 m benthic layer the most, whereas the fish preferred the 0–3 m benthic layer in the macrophyte-poor lake and reservoir. No differences were found in the depth distribution in pelagic habitats sampled by pelagic gillnets for YOY fish between the water bodies. Older fish usually utilized the surface water layer. Macrophytes influenced the depth distribution of YOY fish in benthic habitats, where their density maximum shifted deeper in the macrophyte-rich lake when fewer macrophytes were present in the shallowest benthic depth. In lakes, YOY fish utilized a wider depth spectrum due to the deeper thermocline when compared to the reservoir. Oxygen and temperature stratification are the main factors influencing fish distribution, whereas macrophyte presence particularly influences the depth distribution of YOY fish in benthic habitats.