Portable X-ray fluorescence (pXRF) spectroscopy is commonly used for testing toxic levels of heavy metals in modern industrial waste sites, and it has seen growing applicability in the context of archaeological survey and soils. In this study, we present the results of our pXRF analysis of surface soils at a historic silver refinery located near Puno, Peru, in the western Lake Titicaca Basin. The results of our analysis identified hazardous levels of antimony (Sb), arsenic (As), mercury (Hg), and lead (Pb) in excavation soils, necessitating the relocation of planned excavation units and the use of personal protective equipment. This study highlights the advantages of rapid, in situ pXRF analysis of surface soils in contaminated industrial archaeology sites to assess potential harm to human health.