Pollution of surface water with heavy metals from industrial activities especially those from scrap yard has caused a major threat to human life exposing man to series of hazard, diseases, disability and consequently death. This study focuses on water quality indices of Owode-Onirin and Lafenwa scrap yard with respect to its physicochemical parameters and heavy metal concentrations by evaluating Heavy Metal Pollution Index (HPI), Metal Index (MI) and Potential Ecological Risk Index (PERI). Fifteen water samples were selected randomly from two locations by purposive sampling methods. Five heavy metals which includes Nickel (Ni), Zinc (Zn), Copper (Cu), Cadmium (Cd), Lead (Pb) were analyzed using Atomic Absorption Spectroscopy and standard analytical procedure were follow to ensure accuracy. One way analysis of variance was carried out to analyse the data. The concentrations of the heavy metals were significantly different between sampling locations. However, the mean concentrations of Cd (0.0121 mg/L) were found to be above the highest permissible value of Standard Organization of Nigeria standards for drinking water (SON 2007) and WHO (Guidelines for drinking water quality: incorporating 1st and 2nd Addlenda. World Health Organization, Geneva, 2004) for drinking water. Although Pb was present in two out of the fifteen water samples with a mean value of (0.0324 mg/L) which was also above the highest permissible value. The mean concentrations of Zn (0.2149 mg/L) and Cu (0.0341 mg/L) are found to be below the highest permissible value of the mentioned guideline while no trace of Ni was found in the water samples across the two sampling locations. The mean HPI 518.55 is far above the critical value of 100, indicates that selected water samples are critically polluted with heavy metals. MI revealed low quality water with mean value 4.83, suggests that the selected water is seriously affected with the present of heavy metal. The Hakanson PERI indicated that of the five heavy metals, the risk coefficient of Zn, Pb, Cu, and Ni had light levels of contamination while the level of Cd contamination posed the most serious potential ecological risk, with an index value between 14.1 and 234. The study concluded that order of magnitude to this five heavy metals contamination is Cd > Pb > Zn > Cu > Ni.