Using Data Envelopment Analysis (DEA), this study compared fisheries production efficiency in the South Sea of Korea and analyzed the impact of marine environmental factors on efficiency shifts. We used production data of 12 regional fisheries cooperatives for 10 years (2013-2022), covering 18 areas from Yeoja Bay (western South Sea) to Jinhae Bay (eastern South Sea). During the analysis period, Yeosu and Goheung fisheries cooperatives achieved high technical efficiencies with fewer producers and lower fishing costs. These efficiencies were linked to the high production value of anchovies (Yeosu) and the production quantity of laver (Goheung). The average technical efficiency decreased from 49.3% in 2013 to 40.7% in 2022, with Tongyeong showing the most significant drop (96.4% to 34.5%). Samcheonpo showed the highest scale efficiency compared to technical efficiency, indicating the need to address technical inefficiencies. Yeosu and Goheung Fisheries Cooperatives, which achieved technical efficiency in the static analysis, were found to have dynamic inefficiencies in the 5-year Window-DEA. Fisheries production efficiency in Jinhae Bay and Yeosu showed a significant negative correlation with the number of oxygen deficient water mass occurrences over the years.