The chemical composition of surface geological materials may cause metabolic changes and promote endemic diseases (e.g., oncological, gastrointestinal, neurological or cardiovascular diseases). The results of a geochemical survey is presented following the guidelines proposed by the International Project IGCP 259 performed on the alluvium of Santiago Island (Cape Verde) and focused on public health issues. Geochemical mapping is the base knowledge needed to determine critical contents of potential toxic elements and the potentially harmful regions in the planet. This work presents maps of baseline values of potentially toxic elements (As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, V, and Zn) in Santiago alluvium and the assessment of their human health risks. According to the results the Cd, Co, Cr, Ni and V baseline values are above the Canadian guidelines for stream sediments (for any proposal use) and for soils (for agricultural and residential proposal uses) and also above the target values of Dutch guidelines. Hazard indexes (HI) were calculated for children and adults. For children (HI) are higher than 1 for Co, Cr and Mn, indicating potential non-carcinogenic risk. For the other elements and for adults there is no potential non-carcinogenic risk. Cancer risk was calculated for Cd, Cr and Ni exposures, for adults and children, and the results are only slightly higher than the carcinogenic target risk of 1 × 10 for adults exposed to Cr by inhalation. However, these results may be underestimated because alluvial contaminants may be indirectly ingested by groundwater and by crop and vegetables consumption.