This study compared and analyzed fish communities and mortality rates based on different survey methods (mesh size and retrieval frequency) of stationary nets, which are actively used in freshwater fish surveys in Korea, and proposed an appropriate survey method. Field surveys were conducted on the mainstream of the Nakdong River from May to June 2022 through a total of 10 times of fyke net surveys. The number of species and individuals collected varied significantly depending on the mesh size of the net (5 mm vs. 15 mm) (P<0.001), and larger species with an average total length of over 9 cm were mainly collected in the 15 mm mesh. However, the number of species (P=0.684) and individuals (P=0.100) collected did not show statistically significant differences depending on retrieval frequency (once/24 hours vs. twice/24 hours). In contrast, the mortality rate of fish differed based on all survey methods (mesh size, P<0.001; retrieval frequency, P<0.05), with mortality decreasing as the mesh size increased and retrieval frequency increased. Fyke nets are one of the standard fishing gears used in freshwater fish research in Korea, and to ensure species diversity, it is recommended to maintain the current standard mesh size of 5 mm. However, reducing the current 48-hour deployment time or increasing the retrieval frequency could lower the mortality rate. Furthermore, future research should focus on the differences in fish communities based on the combination of fishing gears commonly used in Korea to improve fish survey methodologies suitable for domestic freshwater environments.