The dairy basin of the Mantaro River located in the centre of Peru faces serious anthropogenic disturbances as it receives emissions and discharges from the metallurgical mining activity located in the headwaters of the basin and milk contaminated with lead (Pb) and cadmium (Cd) endangers the environmental and human health, especially children. To measure the concentrations of Pb and Cd in milk and the dangers of their consumption in the Peruvian population, 40 milk samples were collected and quantified by atomic absorption spectrometry. The mean concentration of Pb in milk was 15 ± 2.6 µg/kg, which represented 75% of the Maximum Limit (ML), and that of Cd was 505 ± 123 µg/kg, which exceeded the ML by more than 194 times. The estimated weekly intake of Pb for people aged 2–85 years was below the Provisional Tolerable Weekly Intake (PTWI) references, determining risk coefficients (CRD) < 1. Weekly Cd intake was much higher than the PTWIs and CRDs were between 14 and 34, indicating that consumers would experience carcinogenic health effects, with children being at higher risk than adults, therefore, milk from the area is not safe for consumption. Cd would be transferred mainly through the soil (water)-grass-milk pathway, due to its presence in irrigation water and in fertilizers that contain Cd. The main pathway for Pb entry would be air-soil (water)-milk grass, from the fine particles emitted into the air by the mining-metallurgical activity, developed approximately 90 km from the study area.