Performance of the prescribed gear of the European Standard (i.e. 1.5 m deep Nordic gillnet) was compared with gillnets deep enough to cover the whole water column (WWCG) for characterizing fish assemblages in a large and shallow lake (Lake Balaton, Hungary). Differences in species number, relative abundance and biomass, and length distribution of fish were examined in both inshore and offshore habitats of the lake. Nordic gillnet samples provided comparable information to that of WWCG for both species richness and abundance and biomass of benthic species. However, substantial differences were found between the two net types in the representation of pelagic fish species (i.e. bleak, razor fish and asp). Overall, the WWCG provided different information with more precise (less variable) data on fish assemblage structure than the Nordic gillnet. Results suggest that identification of neither horizontal nor vertical gradients in within lake fish assemblage structure can be guaranteed with the Nordic gillnet alone even in such shallow lakes, like Lake Balaton. It was concluded that benthic Nordic gillnet samples should be complemented with information on fish occurring in the upper water layers (i.e. pelagic species) even in very shallow lakes either by using pelagic or floating gillnets or by whole water column gillnetting.