Activities at seaports could contribute to ecological hazards such as water pollution. In this study, the environmental impacts of shipping activities at Apapa Bay, Lagos, Nigeria, in relation to the water's physicochemical and potentially toxic metal characteristics, were investigated. Water and sediment samples were collected at four different points, each from four different terminals in Apapa Bay and, similarly, at Takwa Bay, which served as control due to its non-use for shipping. The surface water of the Apapa bay was characterized by the following ranges: 26.35–27.38ºC, 7.03–7.85, 1100–1588 µScm− 3, and 77.28–72.85 ± 0.41 mg/L, for temperature, pH, conductivity, and total alkalinity respectively. The biochemical oxygen demand, BOD5, and the chemical oxygen demand, COD, values 72.4–36.5 mg/L and 199.1–236.7 mg/L, respectively, were above the permissible limits. Low concentrations of phosphate, 0.363–0.652 mg/L, and sulphate, 36.92 ± 14.10–11.10 mg/L were recorded. Potentially toxic metals concentrations ranged: Cd (1.210–3.024 mg/kg); Fe (30.000–35.625 mg/kg); Pb (1.756–65.902 mg/kg); and Cu (10.859–13.423 mg/kg) and were compared with Takwa bay concentrations: 0.600 mg/kg; 6.876 mg/kg; 8.585 mg/kg and 10.859 mg/kg. Different Sediment Quality Guidelines (SQGs) were applied to assess the metal toxicity risk. Significant (p < 0.05) correlations were observed among Cd, Pb, Fe, and Cu suggesting similar sources for the metals. The SQGs classified Apapa Bay as heavily polluted in terms of Cd and Fe and non-polluted with Pb and Cu. These findings provide baseline data for future policies protecting Apapa Bay marine environments.