Contamination of aquatic environment is increasing and has been associated with indiscriminate discharge of solid wastes and effluents generated from industrial, domestic and agricultural activities. These wastes and effluents contain harmful substances, such as metals, which constitute a major problem on the quality of the Nigerian coastal water. This study evaluated the impacts of heavy metals on the water and sediment quality of Ologe and Badagry Lagoons, South-West Nigeria. The heavy metals (Cr, Cd, Cu, Zn, Pb and Fe) in water and sediments was analyzed with atomic absorption spectrophotometer (AAS) using standard protocols. The pollution index (PI) indicated that Cd and Pb had significant effects on the water quality of Ologe and Badagry Lagoons. The metal indices (MI) with Cd, Pb and Zn exceeded the threshold level of (MI > 1). The enrichment factor (EF) indicated extremely contamination with Cd and Pb; significantly contamination with Cr and Cu and very highly contamination with Zn in the sediment of Ologe Lagoon (OL), while the EF in the sediment at Badagry Lagoon (BL) revealed significant enrichment. EF values decreased in order: Cd > Pb > Zn > Cr > Cu in Ologe Lagoon and Zn > Pb > Cr > Cu > Cd in Badagry Lagoon. The sediment pollution index (SPI) values of 174.6 in OL and 57.98 in BL that exceeds 20 are classified as toxic. The geo-accumulation index (Igeo) values for all metals fall in class 0 indicating no pollution, except for Cd that falls within class 1 exhibiting unpolluted to moderate pollution in Ologe lagoon. The calculated mean Effect Range Median quotient (m- ERM-Q) and mean Probable Effect Level quotient (m- PEL-Q) indicated that all metals discharged in the sediment of Ologe and Badagry Lagoons have a 12% and 25% probability of being toxic, respectively. The potential ecological risk factor of heavy metals in the sediment exhibited low ecological risk, except for Cd that indicated moderate ecological risk in Ologe and Badagry Lagoons. These degree of contaminations of the water and sediment with heavy metal beacons for intense strategic biomonitoring due to health concern, as local inhabitants use these lagoons for various economics purposes such as fishing, crop irrigation, dredging, discharge source for industrial effluents and other domestic activities.