This study was conducted to determine the health status of three water bodies (Badagry Creek, Ologe Lagoon and River Owo) because of the large amount of effluent they receive from industries around Lagos as well as the services they provide to sustain the large human population in an emerging mega city like Lagos. Water, sediment and fish samples were collected monthly from the three water bodies between January and December, 2018. Standard methods were used for the analysis of physico-chemical parameters, heavy metals, length-weight relationship, condition factor, fish diversity indices, sediment pollution indices, ecotoxicology of heavy metals in sediment and potential ecological risks as well as health risk assessment of heavy metals. The geoaccumulation index (Igeo) of heavy metals in sediments of the sampling sites ranged from − 12.14 to -0.38. The mean quotients using the probable effect level (m-PEL-Q) are 3.91 x10-4, 4.77 x10-4 and 7.87 x10-4 for Ologe Lagoon, Badagry Creek and River Owo respectively. The trend was the same with mean quotients using effect range-median (m-ERM-Q). The estimated daily intake (EDI) ranged from 0.00 mgkg-1day-1 in Pb from River Owo to 1.15 x10-3 mgkg-1day-1 in Fe still from River Owo. The range of values of the target hazard quotient (THQ) of the metals in Badagry Creek, River Owo and Ologe Lagoon are 1.23x10-4–1.65x10-2, 0.00–1.64x10-2 and 5.76x10-5–1.65x10-2 respectively. The study showed that the three aquatic ecosystems are healthy but require regular monitoring to promptly detect sudden changes in their health status.