This study was conducted to determine the health status of three water bodies (Badagry Creek, Ologe Lagoon and River Owo) exposed to varying degrees of sand mining activities and industrial pollution. Water, sediment and fish samples were collected monthly from the three water bodies between April 2019 and March 2020. Standard methods were used for the analysis of physico-chemical parameters, fish diversity indices, length-weight relationship, condition factor, sediment pollution indices, ecotoxicology of heavy metals in sediment, potential ecological risks and health risk assessment of heavy metals. Positive matrix factorization (PMF) was used to identify and quantify metal source. Shannon’s diversity index (H′) and condition factor varied between 2.03–2.37 and 0.84–4.86 respectively. Enrichment factor had a range of 4.05×10−4–8.65×10−1, while geoaccumulation index varied from −12.14 to −0.38. The mean quotients using the probable effect level (m-PEL-Q) are 3.91×10−4, 4.77×10−4 and 7.87×10−4 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 dietary intake ranged from 0.00 mg/kg/day in Pb from River Owo to 1.15 × 10−3 mg/kg/day in Fe still from River Owo. The range of values of the target hazard quotient of the metals in Badagry Creek, River Owo and Ologe Lagoon are 1.23×10−4–1.65×10−2, 0.00–1.64×10−2 and 5.76×10−5–1.65×10−2 respectively. PMF identified three sources of metal into the aquatic ecosystems: agricultural, industrial and geological inputs. The study showed that the three aquatic ecosystems are healthy but require regular monitoring to promptly detect sudden changes in their health status.
