Inland freshwaters have been recognized as an important component of the global carbon budget; however, the contribution of small streams, especially those draining agricultural watersheds, is not well understood. Open-canopy streams draining row-crop agriculture (i.e., maize and soybeans) in the Midwestern United States are assumed to be dominated by autochthonous production; however, crop detritus may comprise an important but overlooked allochthonous resource, particularly post harvest. In addition, transgenic crop detritus, such as maize that is modified to express insecticidal Cry proteins (i.e., Bt maize), may enter aquatic ecosystems with unknown effects. My dissertation research quantifies organic carbon cycling in Midwestern agricultural streams, and examines the fate of Bt maize detritus in these systems. I found that agricultural streams are less retentive of organic carbon compared to relatively pristine, forested streams, yet they are biologically active, with high light availability and elevated nutrient concentrations fueling production and respiration. The dominant forms of allochthonous organic matter in agricultural streams (i.e., maize leaves and grasses) decompose along a continuum due to differences in substrate quality (i.e., lignin and nitrogen content). Thus, similar to the processing continuum in forested streams, allochthonous detritus in agricultural streams is available for microbial and invertebrate consumption over a sustained period of time. In assessing the fate of Bt maize detritus in streams, I found no influence of genetic engineering on maize decomposition, but that Cry proteins consistently leach from submerged detritus into the water column. I also detected dissolved Cry proteins in agricultural streams and subsurface tile drains in the field throughout the year, even though laboratory microcosm experiments suggest that Cry proteins are rapidly degraded by water-column microorganisms and/or are tightly adsorbed to stream sediments. These results suggest the presence of multiple and/or temporally-consistent sources of Cry proteins to agricultural streams. Overall, my research demonstrates that agricultural streams are important processors and transporters of organic carbon to downstream ecosystems. In addition, understanding the fate of transgenic maize detritus and associated Cry proteins in agricultural streams provides a necessary first step in investigating whether Bt maize may affect aquatic organisms and ecosystem processes.