Arsenic (As) contamination of drinking water is a worldwide problem. The natural origin of As, its mobility, and transport are of paramount interest in Bolivian Altiplano due to its presence in mineral deposits, brines, hot springs, and volcanic rocks. In this study, a geochemical spatial–temporal approach was used to understand the sources and factors that regulate the mobilization and fate of As in water bodies as well as sediments of Lower Katari Basin (LKB). The study reveals that high levels of As (288 µg/L), boron (B) (2473 µg/L), manganese (Mn) (7259 µg/L), and high salinity (23850 µS/cm) are present in shallow drinking water wells, which exceed the guideline values of the Bolivian regulation (NB-512) and WHO. Seasonal changes (mean monthly rainfall in the dry and rainy period: 6–89 mm) and their impact on water quantity (0.9–5.1 m3/s), in addition to the load of solids and liquids of residual origin (Pallina River), pose health risks for the communities at the banks of the Katari River. The hydrogeological study indicates that the groundwater flows from southeast to northwest (SE–NW), which indicate interaction between groundwater and surface water in this region. The spatial distribution of As varies considerably due to geological characteristics of the area as well as due to the heterogeneously distributed evaporites in the sediments (alluvial, fluvial-lacustrine); however, the highest concentrations of As are observed in the alluvial sediments of the northern region. Sequential extraction (BCR) of sediments along with geochemical modeling (mineral saturation indices) indicates that iron (Fe) and aluminum (Al) (hydr)oxides are the most important adsorbent minerals of As in the central and southern region of LKB. The hydrochemistry of water bodies in LKB is strongly influenced by the interaction with the sediment constituents and by the spatial–temporal variations. Therefore, the determination of the distribution of As among the different geochemical fractions was useful to find the relative proportions of As transported by different chemical mechanisms (adsorption/dissolution) and their spatial–temporal variation.