Heavy metal pollution is a serious issue of concern worldwide because it can bioaccumulate in aquatic organisms and transferred through the food chain to harm humans. Information on the heavy metal pollution of aquatic ecosystems is essential to protect life. Therefore, this study was undertaken to determine the physico-chemical parameters of surface water, soil particle distribution (SPD) and heavy metals in two shellfish species in Liverpool axis of Badagry Creek, Lagos State, Nigeria. Twelve physico-chemical parameters and four heavy metals were studied using standard methods. The results showed that maximum temperature was 31.0±1.00˚0C; turbidity, 118.00±50.90NTU; dissolved oxygen (DO), 13.3±3.8mg/l; dissolved carbon dioxide (COD), 67.7±19.1mg/l; total hardness, 173.0±63.1mg/l; conductivity, 39.2±12.2μS/cm and chloride was 2.0±0.7mg/l. Water quality parameters showed significant spatial variations (p<0.05) among sample stations. Pearson’s correction matrices revealed high correlation of DO with nitrate (r = 0.61), total hardness (r=0.62) and COD (r=0.52) at p<0.05. The heavy metal concentrations (mg/kg) in the shellfishes, Callinectes pallidus and Farfantepenaeus notialis were: lead, 0.05±0.05 and 0.04±0.02; copper, 2.03±0.17 and 0.84±0.18; zinc, 3.51±0.44 and 1.99±0.2 and cadmium, 0.02±0.02 and 0.03±0.04 respectively. These levels were not above the WHO standards (for heavy metals in fish and shell fish). The sediment particle distribution (SPD) showed that Liverpool Jetty had 19.05% coarse sand and 43.91% fine sand, while Apapa Jetty had the highest amount of clay 45.29% in the environment. Heavy metals in shellfishes were above the WHO standards.