Recent residential and industrial effluents had triggered the need to continually monitor and assess the hydrochemistry and pollution index of Lagos coastal waters and sediments in Southwest Nigeria. To assess environmental contamination in the Lagos coast, twenty stations (with a recent report of anthropogenic activities) were selected, to determine the concentrations and distributions of hydro-chemical characteristics, heavy metals and total organic content (TOC). The hydro-chemical characteristics (pH; temperature; dissolved oxygen; electrical conductivity; salinity; total dissolved solids; sulphate, chloride, phosphate, nitrate, ammonia, sodium and potassium) of water samples from all the stations studied are within desirable levels for healthy marine ecosystems (except for low (<6) pH at station 8 (Ikorodu Port); station 10 and 11 (Mid Lagoon); station 16 (Badore) and station 19 (Ikosi). The concentrations of heavy metals present in the studied area followed the sequence: Fe > Mn > Cr > Zn > Pb > Cu > Cd. The increased TOC concentrations of the representative short sediment core with depth at station 4 (Iddo) and station 15 (Ikota) suggest record of anthropogenic organic pollutions at the stations. The calculated contamination factor (CF) showed extremely severe contamination (CF > 6) of cadmium (Cd) at station 3 (Ijora), station 4, station 5 (Okobaba), station 6 (Unilag), station 7 (Agboyin) and station 12 (Egbin). The pollution load index (PLI) pointed out high pollution risk (PLI > 1) to the marine ecosystems at Ijora; Iddo and Okobaba, which necessitate regular and continuous monitoring of the coastal waters and estuaries of the Southwestern Nigeria to ensure food security and the safety of the marine ecosystems. The outcome of this study will sound alarm on the increasing levels of inorganic and organic pollutants in the Lagos coastal waters. Southwest Nigeria.