Environmental pollutants significantly impact health and quality of life. High levels of harmful metals in drinking water, vegetables, and soil can accumulate in the body, leading to serious health issues. In Gilgit-Baltistan, Pakistan, the prevalence of cancer is notably high, and heavy metals are considered among the possible risk factors. In this study, the distribution of heavy metals, e.g., Cd, Mn, Cu, Cr, and Ni, in the drinking water, vegetables, and soil in the Gilgit and Skardu Districts was assessed. A geo-accumulation index was combined with a deterministic technique to examine potential carcinogenic and non-carcinogenic impacts on human health. Cr and Ni levels in drinking water exceeded the permissible limits from both districts. Drinking water had a HQ > 1 for Cd, Cr, Ni, and Mn, posing significant non-carcinogenic health effects. The lifetime cancer risk (LCR) by drinking water for Cd, Cr, and Ni in Gilgit (0.0087, 0.55, and 0.0048) and Skardu (0.071, 0.21, and 0.014) indicated a considerable cancer risk (>1 × 10⁻⁴) for adults. The cancer risk for vegetable intake was observed within the safe limit, while LCR_ingetsion > LCR_dermal and LCR_inhalation for the soil samples in both regions. These findings highlight the need for regular monitoring, enhanced waste management, and advanced purification methods to reduce cancer risk, lower heavy metal contamination, and safeguard public health in the region.