The distribution of freshwater fish is influenced by food availability, habitat heterogeneity, competition, predation, trophic state, and presence/absence of macrophytes. This poses a challenge to monitoring, and researchers have been struggling to develop accurate sampling methods for obtaining a better understanding of fish communities. We compare fish community composition, richness, and diversity in 56 Danish lakes using data obtained by gillnetting in different lake zones and near-shore electrofishing, respectively. On average, electrofishing captured more species than offshore gillnets, but not more than littoral gillnets. Overall, the different fish sampling methods showed consistency as to fish community structure, but noticeable differences in community–environment relationships. Lake area was the best predictor for fish species richness in the littoral samplings, while it was poor for offshore samplings. Electrofishing was more efficient than gillnets at catching pike (Esox lucius), eel (Anguilla anguilla), and tench (Tinca tinca), whereas pelagic gillnets were better for catching pikeperch (Sander lucioperca) and perch (Perca fluviatilis). Independently of methods, the total number per unit of effort and weight per unit of effort were generally positively related to summer chlorophyll a, and, for offshore nets, negatively related to average depth. Our results show that sampling restricted to specific habitats within the lakes does not provide a representative of the whole-lake fish community, as all methods miss some important species that other methods capture. However, electrofishing seems to be a fast alternative to gillnets for monitoring fish species richness and composition in littoral habitats of Danish lakes.