Background <p>Ologe Lagoon is one of the freshwaters in Lagos State, Nigeria, that is continuously inundated with anthropogenic pollution such as sand-dredging, indiscriminate waste disposal, open defecation, and effluents disposal from manufacturing industries. The aim of the study is to isolate from the Ologe lagoon sediments and water hydrocarbon degrading heavy metal tolerant bacteria with the capability of producing biosurfactant.</p> Methods <p>On-site, three sampling points were identified. Water and sediments were collected from the Human-activities site (OLHAW/OLHAS), Industrial-contaminated site (OLICS/OLICW), and the presumed-undisturbed site (OLPS/OLPW). Hydrocarbon (HC) degrading and heavy metal (HM) tolerant bacteria were isolated by continuous enrichment of samples on crude oil mineral salt medium (MSM) fortified with heavy metals such as cadmium, lead and nickel over 30 days of aerobic incubation. The identity of isolates was confirmed using the 16&#xa0;S rDNA Sanger-sequencing. Growth of isolate on medium were determined over 30-days; hydrocarbon degradation was monitored using gas chromatography flame ionization detector (GC-FID). Heavy metal tolerance and biosurfactant-producing capabilities of isolates were determined using hemolytic, oil spread and blue agar test.</p> Results <p>Overall, 15 bacterial isolates were identified from the lagoon water and sediment. Based on their effective hydrocarbon degradation and heavy metal resistant capabilities strain OLW3, OLW6 and OLW15 were selected. Molecular identification of isolates showed that strain OLW3, OLW6 and OLW15 were <i>Alcaligenes aquatilis</i>, <i>Alcaligenes faecalis</i> and <i>Rossellomorea marisflavi</i>. The growth dynamics of OLW 3 on medium showed degradation rate of 0.056 ± 0.02 mgL⁻¹d^− 1, degradation rate constant of 6.43 ± 0.18 d^− 1, degradation half-life of 12.49 ± 0.16. The isolates showed overall percentages degradation between 54% and 85% while tolerating heavy metals. The statistical analysis of the emulsification indices (E24%) done using one-way analysis of variance (Friedman multiple test comparison) and showed a mean significant different (<i>P</i> &lt; 0.05) among the dataset. Post-hoc analysis by Dunn’s multiple comparison showed pairs were different with higher level of difference between OLW 6 and OLW 15 dataset.</p> Conclusion <p>Effects of anthropogenic activities on freshwater health is severe. The continuous pollution made lagoon source of Hc-degrading, HM-tolerant microbes. The isolates can serve as biological agents for environmental reclamation.</p> Clinical trial number <p>Not applicable.</p>