A variety of gears and analytical methods can be used to characterise lentic fish assemblages; however, the combined influence of gear type and analysis can affect conclusions about assemblage patterns. Fish assemblages sampled with night electric fishing, gillnets and trapnets from 153 lakes were evaluated using summary indices of species composition, pairwise community similarity comparisons and multivariate ordination. For a given amount of effort, electric fishing had the highest species richness, while gillnets had higher diversity and evenness. Pairwise comparisons between gears revealed that (1) richness was positively correlated among all gears, (2) diversity and evenness were generally not correlated across gears and (3) electric fishing and trapnets captured more similar species than all other pairwise comparisons. Gear-specific multivariate correlation and ordination revealed that gillnet and electric fishing samples more similarly characterised variation in assemblages among lakes, while trapnets characterised assemblages along different gradients of species composition. These results indicate that either electric fishing or trapnetting can be used when assessing shallow-water assemblages for diversity or evenness, gillnets and either electric fishing or trapnets should be used for whole-lake assessments, and either gillnets or electric fishing should be used when evaluating regionwide variation in lake assemblages.