Abstract: Establishing fishery-solar complementary photovoltaic (PV) power stations is an important measure for China to realize its “Dual Carbon” goals, and the ecological effects of PV power stations have received widespread attention. Based on a 54 MW fishery-solar complementary PV power station in Jiangsu Province, this study selected fish ponds with different PV shading conditions and power-frequency electromagnetic fields as the study areas and established 18 sampling points. We used methods including t-test, analysis of covariance, and linear regression to systematically analyze the independent effects, potential driving mechanisms, and influence patterns of PV shading and power-frequency electromagnetic fields on water quality indicators in fish ponds. The results showed differences in water quality indicators such as water temperature, pH, dissolved oxygen (DO), and chlorophyll a (Chl-a), while the differences in conductivity, NH₃-N, chemical oxygen demand (COD), and total organic carbon (TOC) were relatively small. A linear relationship was found between Chl-a and DO. Changes in light availability induced by PV shading were significantly correlated with Chl-a and DO, and PV shading was the dominant factor causing changes in DO. Within the study area, power-frequency magnetic fields (0.0103–0.0934 μT) showed no significant correlation with any water quality indicator, while power-frequency electric fields (22.26–61.72 V/m) showed a positive trend with conductivity but without linear relationship. This study clarified the impacts of low-intensity electromagnetic fields in fishery-solar complementary PV power stations on aquaculture water quality indicators, thereby promoting their green and sustainable development.