Milk of cattle and goat was collected from various localities of Faisalabad, Pakistan. Heavy metal concentration in milk was determined by atomic absorption spectrophotometer. Milk from both of the species was found richly contaminated with cadmium (Cd), chromium (Cr), nickel (Ni), and lead (Pb). Lead concentration in the milk of goat was significantly higher as compared to cattle milk. Quantitative structure activity relationship (QSAR) models were suggested to predict the residues of unknown heavy metals in the milk of cattle and goat using their known physicochemical properties such as molecular weight (MW), melting point (MP), and boiling point (BP) as well as the milk characteristics such as pH, % fat, and specific gravity (SG) of both of these species. The analysis revealed good correlation coefficients (R2 = 0.759) and (R2 = 0.876) for cattle and goat QSAR models, respectively. This analysis indicates the need to construct species specific QSAR models for residue prediction. The coefficients for SG for the studied metals were higher in both cattle and goat milk. This suggests that SG is a better determinant for heavy metal residue prediction in the milk of these animals. Risk analysis was conducted based upon the determined heavy metal residues and their provisional tolerable daily intakes. The daily intake of Cd, Cr, and Pb was found to be 1.6, 27, and 116 times higher, respectively, in cattle milk and 1.8, 29, 262 times higher respectively, in goat milk. This intake of heavy metal contaminated milk might pose health hazards to humans in this locality.