The accurate estimation of fish assemblages is highly dependent on the sampling gear used for sampling. We used data from 15 sampling sites along the Nakdong River, which is a large river in South Korea, to identify differences in assemblages and sizes of freshwater fishes collected with either cast nets or gill nets, the two most commonly used sampling gear in South Korea. The two gears differed in the fish assemblages they captured, with more species caught by gill nets. Further, due to its tighter mesh size, the cast net caught significantly smaller fishes than the gill nets (independent t-test, p<0.05). We found the cast net to be appropriate for species that inhabit shallow (less than 2 m) and open water, but inappropriate for deep water, habitats with plant beds, and nocturnal species. Thus, cast net sampling is not efficient in a large river environment, and a combination of sampling methods is more suitable for understanding fish assemblages in such habitats. In general, appropriate selection of fishing methods to specific habitats is necessary to improve data quality and minimize the misrepresentation of environmental conditions.