Pollution by heavy metals in aquatic ecosystems has become the central focus of environmental research, due to the threat it poses to consumers of fishery sources. This study seeks to assess the levels of accumulation and potential human risk associated with heavy metals in Chrysichthys nigrodigitatus from Ologe and Badagry lagoons Southwestern Nigeria. The metals (Cr, Cd, Fe, Ni, Cu, Zn, and Pb) in fish samples were analyzed with atomic absorption spectrometer (AAS), while the estimated daily intake (EDI), target hazard quotient (THQ) and target cancer risk (TR) were also estimated. All metals in the muscles of C. nigrodigitatus were below the WHO/FMEnv guideline. Pearson correlation coefficient of heavy metals in muscle of C. nigrodigitatus showed significant correlation (p < 0.05) between Cu and Pb (r = 0.990^*), Cr and Cu (r = 0.962^*), Cr and Pb (r = 0.985^*). The target hazard quotient (THQ) of the metal decreased in the following order: Pb > Zn > Cd > Fe > Cu > Cr > Ni and the hazard index (HI) risk values were 0.203 and 0.140 at Ologe and Badagry lagoons respectively. The THQ for all heavy metals estimated across both lagoons were all less than 1. The target cancer risk (TR) observed the highest values of 4.3 × 10^-5and 5.20 × 10^-5for Ni at both Ologe and Badagry lagoons respectively. The THQ had no adverse health effects from the consumption of fish. However, target cancer risk (TR) due to Pb and Ni exposure through fish consumption may increase the probability of developing cancer in the future. The biomonitoring of metal accumulation in tissue of Chrysichthys nigrodigitatus underscores the need for periodic monitoring of the lagoon.