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Selenium (Se) is an essential nutrient for human health. To systematically study the distribution and control factors of Se in the local environment of Shiquan County, known for its characteristic agricultural products, rock, topsoil, well water and crop samples were collected. The contents of total Se and heavy metals in the samples were determined by instrumental analysis (ICP-MS, XRF and AFS). The results show that Se is significantly higher in the Lower Silurian Daguiping Formation, Carboniferous Maping Formation, and Cambrian-Ordovician Donghe Group in the study area. Lithology is the main factor that controls the Se content of rocks. The average content of total Se in the topsoil of Shiquan County was 0.68 ± 2.30 mg/kg (n = 678), which was higher than the average Se content in the soil of the main agricultural areas in China. Se-rich parent rocks are the main factor affecting the distribution of Se in the soil. The Se content of the surface soil gradually decreases with increasing altitude. Soil slope does not affect Se concentration. There was a significant positive correlation between soil Se concentration and pH value in the study area, and the distribution area of neutral soil was consistent with that of Se-rich soil. Mn-oxides affect Se concentrations in neutral soils in the study area. The average Se content in groundwater in the study area was 0.98 ± 0.20 mg/kg and the weathering of the parent rock was the source of Se in the groundwater. The Se content of vegetable crops (pepper, radish) in Shiquan County is typically higher than that of rice and corn. However, the concentration of heavy metals in vegetable crops (pepper, konjac, and radish) is severely excessive, and they should not be selected as Se-rich crops. This research is conducive to rational development and utilization of Se-rich soils.
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