Impurities found in fish have been a major cause of disease and illness to consumers. This study's objective was to evaluate the total aflatoxin, heavy metal and microbial load in two frozen fish: Scomber scombrus and Clupea harengus from two (2) cold room facilities in Omu-Aran and Ilorin. Heavy metals, aflatoxin and microbial load were investigated using standard methods. Health risk was also determined using health risk index (HRI), daily intake of metals (DIM), and health quotient (HQ), and total toxicity of metals (TTM). Cd, Cu, Ni, Pb, Mn and Cr did not differ significantly (p>0.05) in both species from both locations. Nickel was lower than the recommended limit by World Health Organization (WHO). Level of Mn and Cr were higher in both species. Mn load was higher in the muscles of the sampled fish than in the gills from September through to November with highest value of 1.26±0.08 and 1.30±0.12 obtained for S. scombrus and C. harengus. Highest concentrations of all metals was observed in the gills except manganese and copper [Cd = 0.03 (S. scombrus), Cr = 1.22±0.13 (S. scombrus), Ni = 0.025±0.04 (S. scombrus), Pb = 0.06±0.02 (S. scombrus)]. HRI was > 1 in the different age groups for the different metals. TTM was > 1 in both species. Total aflatoxin level was higher in the gills (4.25 – 5) ppb than in the muscle (1.5 - 3) ppb for both locations respectively. Vibrio spp. and non-coliform bacteria were high in both species from both locations. The study concludes that heavy metal loads (Mn, Cd, Cu, Cr, and Ni) were more than the permitted limitations imposed by FAO, WHO and EU legislation for fish and fish products placing consumers at health risk.