Based on 40 years of routine water quality monitoring data from Shenzhen Bay and special intensive monitoring since 2021, we analysed the spatiotemporal variations in nitrogen and phosphorus pollution. The results indicate serious levels of nitrogen and phosphorus pollution in Shenzhen Bay. Although recent trends show a decline in concentrations of inorganic nitrogen and reactive phosphate—with the annual average concentration of inorganic nitrogen dropping below 1.0 mg/L since 2020 and reactive phosphate levels near the bay mouth decreasing to approximately 0.020 mg/L—the overall water quality still does not meet China’s Class IV seawater quality standards. Additionally, water quality is poorer during the rainy season, with the average summer concentration of inorganic nitrogen being over 25% higher than in spring and autumn. The water quality is primarily influenced by land-sourced pollutants and tidal effects, generally, with the concentration of DIN and DIP decreased from the estuary of the Shenzhen River, the main seagoing river, to the bay mouth. Near the river’s mouth, concentrations of inorganic nitrogen and reactive phosphate are approximately six and four times higher, respectively, than those near the bay mouth. Due to current emission standards and sewage disposal methods, the proportion of nitrate nitrogen in DIN has significantly increased, exceeding 80% since 2020. To improve the water quality of Shenzhen Bay and to reduce pollution inputs, coordinated land and marine development activities are recommended.