This study examined ten heavy metals in five species: Macrobrachium vollenhovenii, Penaeus monodon, P. notialis, Chloroscombrus chrysurus, and Pseudotolithus typus, from Makoko floating slum, Lagos Lagoon to discern their bioaccumulation potentials, sources of origin, and health implications. The concentrations were in this order: Fe (4.172–10.176) > Zn (1.310–5.754) > Mn (0.475–2.330) > Cu (0.238–1.735) > Pb (0.121–0.391) > Cd (0.055–0.283) > Co (0.056–0.144) > Ni (0.039–0.121) > Cr (0.022–0.095) > As (0.003–0.031) mg/kg. The MPDI denotes “low toxicity,” and the BAF/BSAF revealed that benthic species had higher bioconcentration potentials. Multivariate analyses revealed that heavy metals exhibited mutual relationships during chemical transport, and their sources were both geogenic and human-induced. The HI values were below 1, and the TCR values were below the threshold of 1 × 10−4. This suggests that the probabilities of noncancer and carcinogenic risks in human populations due to long-term consumption of the evaluated species are unlikely.