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.

Shansha Bay, southeastern China, is a typical semi-enclosed bay facing intense anthropogenic pressure, with mariculture production reaching approximately 660,000 tons annually, predominantly driven by the large yellow croaker (Larimichthys crocea) industry. To assess how these pressures influence biodiversity detection, we employed eDNA metabarcoding targeting the 12S rRNA gene to survey fish diversity across 10 sites, integrating both surface water and sediment matrices. A total of 40 species belonging to 16 orders, 27 families and 32 genera, were identified. Among them, L. crocea, Bostrychus sinensis, Clupanodon thrissa and Siganus fuscescens are the dominate species, which comprised over half of all OTUs. Comparison with historical trawl surveys revealed 30 newly recorded species, including the Japanese eel (Anguilla japonica) and oarfish (Regalecus glesne). Alpha diversity was low (Shannon: 0.69–1.93), with significant spatial disparities driven by freshwater runoff and hydrodynamics. While eDNA effectively captured the dominance of cultured species like L. crocea, the extreme biomass signal poses challenges for detecting wild populations. Our findings underscore that a multi-matrix eDNA approach is crucial for accurate biodiversity assessments in aquaculture-dominated coastal ecosystems, although distinguishing wild stocks from aquaculture-derived DNA remains a critical methodological hurdle.