Pesticides are used to control pests in a variety of habitats including agricultural lands, forests, commercial lands, and domestic properties. Pesticide transport from such habitats to surface waters leads to environmental contamination. The objectives of this research were to compare the pesticide types present in the water-column and bottom-sediments of rivers flowing through intensively-managed and semi-natural habitats and to examine the extent of variations in MCPA and 2,4-D concentrations in the sediments that could be explained by measured laboratory parameters such as Kd, sediment organic carbon content and particle size distribution. This study screened water-column and sediment samples for 160 pesticide compounds which is substantially greater than what has been typically included in Prairie surface water research. River contamination primarily arises as a result of current-use pesticides applied in agricultural and urban habitats. For most compounds detected, there was no significant correlation between their concentrations detected in water and sediments, suggesting that pesticide concentration in the water-column is a poor indicator of the presence of pesticides in sediments. Pesticide mixtures were more common in water (72%) than sediments (51%) and dominated by broadleaf herbicides. The concentrations of pesticide mixtures detected in water never exceeded their calculated threshold value for the Pesticide Toxicity Index, indicating that the presence of pesticides in Prairie rivers continue to pose no significant risks to freshwater organisms. The batch-equilibrium study found that regardless of the lower sorption to sediments, more frequent presence of MCPA in the water-column allowed for greater opportunities for MCPA to partition to sediments compared to 2,4-D. Thus, the water-column loadings of those compounds, and not sediment characteristics, are the driving force for determining their frequencies and concentrations in sediments. Since this study found that herbicides co-applied with MCPA and 2,4-D were often detected in river waters, future monitoring studies should focus on a wide variety of active ingredients that are co-applied with the top ranked active ingredients. Also, additional monitoring studies should focus on rivers flowing through urban and agricultural lands. Future batch-equilibrium studies could incorporate different concentrations of MCPA and 2,4-D mixtures to further examine chemical sorption under different environmental conditions.