Introduction: Heavy metal content of aquatic ecosystems is attracting global attention because of the ecological and human health risks associated with high levels of these metals in the environment. Aim: This study investigated the heavy metal content of various compartments of Ologe Lagoon in order to ascertain the safety of the consumption of fish and other resources from this water body. Materials and Methods: Samples were collected between June and November 2015, from the stations on monthly basis. Some physico-chemical parameters (alkalinity, salinity, pH, turbidity and hardness) and the levels of five heavy metals (Zn, Fe, Cu, Cd and Pb) in water, sediment, Eichhornia crassipes and a commercially important fish (Chrysichthys nigrodigitatus) were studied using standard procedures. Results: The ranges of values of the metals in sediment were: Fe (431.10±109.75-2560.33±1101.32 mgkg–1), Zn (3.77±2.55-17.29±5.30 mgkg–1), Cu (7.45±6.55-35.21±33.79mgkg–1), Pb (5.98±2.29-12.89±4.22 mgkg–1) and Cd (0.31±0.31-0.88±0.21 mgkg–1). The concentrations of heavy metals (except Cu) in Eichhornia crassipes have exceeded FEPA and WHO maximum permissible limits. The mean concentrations of heavy metals (except Zn) in Chrysichthys nigrodigitatus were above the limit recommended by FEPA and WHO. Conclusion: The study showed that the metal load in the biota of Ologe Lagoon is increasing and this may be harmful to inhabitance of the community, who depend on the services provided by this aquatic ecosystem. Therefore, efforts should be made by all users of the water bodies especially the industries to treat their wastes before discharging them into these aquatic ecosystems.