Similar to the San Joaquin Valley of California, the Canadian prairies are underlain with seleniferous shale and have recently witnessed a significant expansion in irrigated agriculture. The irrigated acreage in the prairies is expected to further increase due to global warming and changes in human use patterns. This raises concerns over potential selenium (Se) contamination in prairie surface waters and risk of adverse biological effects. To test the potential for elevated Se in the prairies, Se concentrations and speciation were examined in surface water, sediments, and sediment porewater in three water bodies in southern Manitoba, Canada, along a north-south transect with a gradient of irrigation and agricultural activities. A selenite addition experiment was also performed in mesocosms in a prairie wetland to assess the risk of increasing Se loading to the prairie waters. Overall, our results indicate that Se concentrations in the prairie waters of southern Manitoba are presently low except during the snowmelt season, that Se speciation is dominated by selenate which is of lower toxicity than selenite, and that if additional selenite is discharged into the prairie waters, it will be quickly removed from the surface water to the sediment. The low Se risk in the Canadian prairies is attributed to high soil drainability and relatively small scale of irrigation at present. The Se problem as being experienced in central California is thus unlikely to occur in surface waters of the Canadian prairies, although Se contamination in ground water is possible should the irrigated acreage continue to increase.