Fish communities differ significantly between the littoral and the pelagic habitats. This paper attempts to define the shift in communities between the two habitats based on the European standard gillnet catch. We sampled the benthic and pelagic habitats from shore to shore in Lake Most and Římov Reservoir (Czech Republic). The 3 m deep pelagic nets were spanned across the water body at equal distances from two boundary points, where the depth was 3.5 m. The benthic community contained more fish, more species, and smaller individuals. The mild sloped littoral with a soft bottom attracted more fish than the sloping bank with a hard bottom and less benthos and large Daphnia. The catch of the pelagic nets was dominated by eurytopic fish—rudd (Scardinius erythrophthalmus) and roach (Rutilus rutilus) in Most and bleak (Alburnus alburnus) in Římov. With the exception of one case where overgrown macrophytes extended the structured habitat, the largest shift from the benthic to the pelagic community was observed only in the first pelagic gillnet above the bottom depth of 3.5 m. Open water catches were relatively constant with small signs of decline towards the middle of the lake. The results indicate that the benthic gillnet catch is representative of a very limited area and volume, while most of the volume is dominated by the pelagic community. This has important consequences for the assessment of the community parameters of the whole lake following the European standards for gillnet sampling design.
