This study investigates the geochemical background and factors influencing the variability of 19 environmentally relevant elements in the soils of Antofagasta, Chile, a region known for its extensive mining activities. Employing robust multivariate statistical techniques on a dataset of 94 soil samples, we identified four main factors explaining 70% of the total variance in elemental concentrations. These four factors reflect the influence of Jurassic volcanic rocks, intrusive rocks, marine sediments, and mafic to intermediate intrusive rocks. Cluster analysis revealed three distinct geochemical populations, each reflecting a unique combination of natural and anthropogenic influences. We established background concentrations for each element within these clusters using robust statistical methods. Geostatistical analysis, employing inverse distance weighted interpolation, produced factor distribution maps that, when integrated with geological data, provided insights into lithological and anthropogenic influences on soil geochemistry. Our findings highlight the complex interplay between natural geological processes, the region's unique arid climate, and anthropogenic activities in shaping the geochemical landscape of Antofagasta. This study contributes to the understanding of geochemical backgrounds in mining-intensive, arid regions and provides a methodological framework applicable to similar environments worldwide.