Rapid warming has considerably impacted fish populations, with responses influenced by traits related to migration and metabolism. However, previous studies on the effects of warming often struggled to isolate warming-specific impacts due to challenges in directly comparing affected and unaffected areas. Investigating the effects of rapid warming caused by nuclear power plants provides a unique and valuable opportunity to address this limitation. In this study, we focused on fish populations at two coastal sites in Japan: one affected by thermal discharge from a nuclear power plant, and the other serving as a control site. We compared fish populations between these two sites. We analyzed changes in abundance and body size, identifying traits that influenced these responses. The results revealed that 18% of species showed significant changes in abundance, while 40% exhibited significant changes in body size. Using a generalized linear regression model, we found that traits such as migratory behavior, trophic level, latitudinal distribution, and average body size were associated with these changes. Migratory and tropical species, in particular, were more likely to increase in both abundance and body size under warming conditions. These results suggest that warming enabled migratory and tropical species to overwinter and establish populations at the warming site. To better understand changes in fish communities driven by global warming along the Japanese coast, monitoring a broad range of species, as demonstrated in this study, would be highly effective. Additionally, focusing on traits related to migration and metabolism can help identify species particularly vulnerable to warming.