Trace elements are loaded to agricultural soils through irrigation, application of pesticides and fertilizers, potentially deteriorating soil quality, and contaminating underlying groundwater resources. In western Texas along the Rio Grande valley, cropland is developed on floodplain sediments of different particle sizes, where intensive irrigation mobilizes the salts, nutrients and trace elements from the agricultural fields. This study focuses on seven trace elements (As, Pb, P, Zn, V, B, and Fe) in soils and natural waters at a pecan orchard in Tornillo, Texas, to understand their geochemical behaviors and toxicity. Soluble forms of these trace elements were predominantly loaded onto soils through irrigation water. Soil amendments also contributed, and were important sources for nutrients Zn and P. Trace element sequestration was examined through sequential extraction, and the acid leachable fractions of soil samples contained much higher concentrations than water leachable salt fractions, suggesting co-precipitation with secondary carbonate and Al/Fe oxyhydroxide phases. Solubility of V and Fe are controlled by redox conditions, and dictated by flood irrigation events and thus fluctuations in groundwater table. Above soils of finer particles, where water infiltration is limited, and salts and pedogenic carbonates mostly accumulate, trace elements also become concentrated, without draining to the shallow groundwater and drainage canals. The trace element concentrations in shallow groundwaters were variable, but generally much lower for P and much higher for Zn than those in irrigation waters or soil waters. Natural soils have surprisingly high concentrations of trace elements, even more so than some agricultural soils, probably due to movement of solutes from shallow groundwaters via the capillary force over much longer timescales under dryland conditions. This interpretation is supported by the finer particle sizes observed at the bottom of the natural soil core. Our study highlights that irrigation has modified the water dynamics, the geochemical conditions, and thus the mobility versus retention of trace elements in soils.