The adoption of genetically modified (GM) crops has occurred rapidly in the United States. The transfer of GM corn byproducts from agricultural fields to nearby streams after harvest is significant and occurs well into the post-harvest year. These corn leaves, stems, and cobs then become a detrital food source for organisms, such as shredders in the stream ecosystem. Considering that the nontarget effects of Bt corn have been observed in some terrestrial organisms, we assessed whether Bt toxins affect an important aquatic organism, juvenile F. rusticus crayfish. Juvenile crayfish were fed six distinct diet treatments: two varieties of Bt corn, two non-Bt controls of herbicide tolerant corn, and two controls: fish gelatin and river detritus. Juveniles were fed these diets while housed in flow-through artificial streams that received natural stream water from a local source. Specific growth rate and survivorship of the crayfish were measured throughout the study. Juveniles fed corn diets grew significantly less and had reduced survival compared with juveniles fed fish gelatin or river detritus diets. Furthermore, juveniles fed one Bt variety of corn (VT Triple Pro®) exhibited significantly less growth than those fed one of the herbicide tolerant varieties (Roundup Ready 2®). Our study shows that corn inputs to streams may be detrimental to the growth and survivorship of juvenile crayfish and that certain Bt varieties may exacerbate these negative effects. These effects on crayfish will have repercussions for the entire ecosystem, because crayfish are conduits of energy between many trophic levels.