Spring Zooplankton Community Structure and Its Relationship with Water Quality Gradients in Representative Nearshore Systems of the Beibu Gulf, China

This study integrated two surveys—one conducted in August 2021 in the Maowei Sea–Beilun Estuary (14 stations) and another in spring 2023 in Qinzhou Bay (16 stations)—to delineate four functional zones (MWS, BLE, WJ, WW). We systematically analysed zooplankton communities and water quality factors and used Structural Equation Modelling SEM to break down the effects of eutrophication on zooplankton into direct and indirect pathways. The results showed that sixteen zooplankton species belonging to six major taxonomic groups were recorded. Copepoda dominated the community, accounting for 50% of the total recorded species. Parvocalanus crassirostris reached a dominance index (Y) of 0.54, higher than historical records (0.35–0.40), indicating increased community homogenization. Salinity increased from 2.0 to 29.6 psu, resulting in community homogenization, and DIN decreased from 1.282 to 0.19 mg/L. Ei averaged 13.49 (MWS) and 12.80 (BLE). Zooplankton biomass rose nearly 7-fold (125 to 880 mg/m3, p < 0.05). SEM revealed a direct inhibitory pathway from eutrophication (−0.36), an indirect pathway via phytoplankton food-quality degradation (−0.14), and one via community high evenness compression (−0.06), for a total of −0.56 (Bootstrap 95% CI significant). The heavy-metal total effect (−0.18) was much weaker. The SEM fit was excellent (CFI = 0.976, RMSEA = 0.038, R2 = 0.68). This study is the first to quantify dual-indicator management thresholds (salinity < 10 psu and DIN > 0.8 mg/L) for early risk warnings in nearshore aquaculture in this region.