Metals are one of the most common pollutants of surface water around the world. The anthropogenic contribution to aquatic metal pollution is of global concern. This study investigates the levels of Ca, Cd, Cu, Fe, Mn, Pb, Ni and Zn in surface water and sediments in the Lagos lagoon (Ibafon-Apapa, University of Lagos waterfront, UWF) and Ogun river catchment at Agiliti-Ketu. The metal concentrations were determined using atomic absorption spectrophotometry. Ibafon-Apapa generally, accounted for the highest concentrations of metals in both water and sediment samples. The ranges of concentrations (µg/g) of metals in sediment samples were: 0.08 ± 0.05–2140.64 ± 1981.54, ND-7.19 ± 7.32, 4.59 ± 2.46–78.95 ± 49.15, 3276.22 ± 2059.57–25,307.60 ± 8759.66, 255.73 ± 98.54–4651.0 ± 1672.60, 19.84 ± 10.23–228.50 ± 84.17, 4.51 ± 4.02–24.45 ± 22.78 for Ca, Cd, Cu, Fe, Mn, Pb and Zn, respectively. Ni occurred in the water and sediment samples below the detection limit. The water and sediments samples from UWF have mean pH values of 7.71 ± 0.07 and 6.61 ± 0.40, respectively, which are higher than that of Agiliti-Ketu (7.65 ± 0.06 and 6.58 ± 0.95) and Ibafon-Apapa (7.60 ± 0.39 and 4.20 ± 0.50), respectively. The highest values for electrical conductivity (EC) was recorded in Ibafon-Apapa (8.54 ± 1.27 μS/cm) followed by UWF (6.50 ± 2.16 μS/cm) and Agiliti-Ketu (0.28 ± 0.40 μS/cm), respectively. The relatively high values of EC and total dissolved solids (TDS) in the Ibafon-Apapa and UWF axis of the Lagos lagoon is an indication of the brackish nature of the lagoon, while the low mean values of EC (0.28 ± 0.40 μS/cm) and TDS (78.0 ± 13.04 mg/L) recorded for Agiliti-Ketu is a pointer to the freshwater attribute of the water. Cd, Mn, Fe and Pb were found to exceed the WHO limit for drinking water. Results were compared with global background values. Cadmium, manganese, iron and lead levels in the water and sediments samples revealed metals pollution. Statistical analysis of variance and t-test were used to analyze the data obtained. Metals pollution source control is recommended.