Selenium (Se) that was once sequestered below the soil surface has been exposed to accelerated weathering conditions in the Western Phosphate Resource Area (WPRA), creating a potential threat to the ecosystem. The goal of this study was to evaluate the impact of an organic amendment (manure) and a sulfur-containing fertilizer on Se availability as determined by plant tissue concentrations and soil water chemistry. Tension lysimeters were used to sample soil water from treated plots. A greenhouse experiment was conducted to study the impact of these amendments on plant uptake of Se in a more controlled environment. A maximum of 7% of the soil water samples collected on any one date exceeded the suggested limit for water consumed by livestock (50 μg Se L−1) within the United States. Significant differences among treatments only occurred in the first sampling date when the mean Se concentration of water samples from the gypsum treatment was higher than in the manure and control treatments. In the greenhouse study, Se uptake by alfalfa (Medicago sativa) was higher than uptake by mountain bromegrass (Bromus marginatus), suggesting that alfalfa should not be planted on reclaimed mine soils within the WPRA. Although the use of organic amendments has been shown to increase the loss of Se through volatilization, our data suggest that it may result in a short-term increase in Se uptake, possibly caused by organic acids outcompeting selenite for soil-binding sites. These results can be used to help design and implement future remediation strategies in the WPRA.