The impact of bio-invasions and abnormal aggregations of marine life on the safety of cooling water systems in coastal nuclear power plants (NPPs) is significant and cannot be overlooked. In this study, we conducted 12 consecutive monthly surveys from September 2022 to August 2023 in the waters near Ningde NPP in Fujian, China, focusing on nekton species composition, dominant species, abundance, biomass, and diversity indices. We conducted statistical analyses to examine potential correlations between the community structure of these organisms and environmental factors. We recorded 120 species of nekton that belonged to 20 orders, 57 families, and 92 genera, including 72 species of fish, 23 species of shrimp, 19 species of crabs, and 6 species of cephalopods. Pearson and redundancy analyses showed that pH, DIP, and inorganic nitrogen were the main environmental factors driving the observed temporal changes in the nekton community structure in the seawater intake area. We also found that May to October is the peak period for nekton abundance and biomass, and during this time, there is a high risk of nekton blocking the cooling water system of the NPP. These results are of practical significance for NPP managers to prevent and control the clogging of the cooling water system by marine organisms, and the diversity and abundance data provide a theoretical basis for bioecological restoration and management of the area around the Ningde NPP.