This study assesses decadal changes (2005–2015) in the trace and heavy metal element contents of soils from four land use types at a desert oasis and also determines associated ecological and health risks. Concentrations of boron, molybdenum, manganese, zinc, copper, cadmium, lead, and mercury increased significantly over the decade. Farmland ecosystems had higher concentrations of soil trace and heavy metal elements than natural ecosystems, but intercropping with alfalfa tended to reduce concentrations. The environmental pollution assessment indicated that soils were moderately affected by human activities, particularly in farmland ecosystems. The potential degree of ecological risk from all elements was moderate, and in relation to land use this risk decreased in the following order: long-term cultivated farmland>newly reclaimed farmlands with monoculture>newly reclaimed farmlands with intercropping>natural desert grassland. Eight soil heavy metals posed potential non-carcinogenic risks, and dermal contact was the major exposure pathway; however, the carcinogenic risk level from soil was acceptable. These results suggest that agricultural activities increased the concentrations of certain soil trace and heavy metal elements and that adopting appropriate farmland management, such as intercropping with alfalfa, limited this increasing trend.