The aim of this study was to compare littoral zone fish assemblage richness, composition, dominance and size patterns between beach seine and gillnets sampling methods in coastal lakes at Tramandaí river, Southern Brazil. Monthly samples were taken in the littoral zones of six coastal shallow lakes (Itapeva, Quadros, Malvas, Fortaleza, Rondinha and Barros). Dominance and similarity analyses showed differences in species composition, numerical abundance and biomass among the sampling methods. Eleven species were dominant, but only one (Psalidodon aff. fasciatus) was dominant to both sampling methods. Beach seines sampled individuals with a total length ranging from 20 to 80 mm, while gillnets sampled individuals with a total length over 100 mm. An assemblage with high species richness, dominated by small fishes was found in the lake’s margins. In contrast, an assemblage with lower species richness comprised of larger fishes was found in inner areas. The methods are complementary in accessing species richness. Beach seine is a better alternative for monitoring programs as it provides reliable data at lower cost. These results may be useful in the sample design of future research or in the monitoring of ichthyofauna.