This study investigated and characterised concentration of some selected metals and metalloids (As, Cd, Cr, Cu, Co, Fe, Mn, Ni, Pb, Sn, V and Zn) present in surface sediments of the Lagos Harbour (LH) and associated Lagos Lagoon (LG) system using a combination of metal extraction and analytical methods within 26 sampling sites including a control (Apese Lagoon, APL). Sampling was carried out using a Van-veen grab sampler on three occasions (dry seasons 2013, 2014; wet season 2013). The total, recoverable and bioavailable fractions were measured separately by X-ray fluorescence (XRF), Aqua regia (AR) extraction with inductively coupled plasma optical emission spectrometry (ICP-OES) and 1 M hydrochloric acid (1 M HCl) extraction with inductively coupled plasma mass spectrometry (ICP-MS) analysis, respectively. Results were compared with National Oceanic and Atmospheric Administration (NOAA)/Canadian Sediment Quality Guidelines (CSQG) and geochemical spatial distribution maps. Threshold effect level (TEL) were exceeded by total concentration of Cu, Zn and recoverable As across the lagoons. Bioavailable As was below TEL while Ni was associated with the ports in the LH.