Corn (Zea mays L.) transformed with a gene from the bacterium Bacillus thuringiensis (Bt) comprises 49% of all corn in the United States. The input of senesced corn tissue expressing the Bt gene may impact stream-inhabiting invertebrates that process plant debris, especially trichopteran species related to the target group of lepidopteran pests. Our goal was to assess risk associated with transgenic corn debris entering streams. First, we show the input of corn tissue after harvest was extended over months in a stream. Second, using laboratory bioassays based on European corn borer [Ostrinia nubilalis (Hübner)], we found no bioactivity of Cry1Ab protein in senesced corn tissue after 2 wk of exposure to terrestrial or aquatic environments. Third, we show that Bt near-isolines modify growth and survivorship of some species of invertebrates. Of the four nontarget invertebrate species fed Bt near-isolines, growth of two closely related trichopterans was not negatively affected, whereas a tipulid crane fly exhibited reduced growth rates, and an isopod exhibited reduced growth and survivorship on the Cry1Ab near-isoline but not on the stacked Cry1Ab Cry3Bb1 near-isoline. Because of lack of evidence of bioactivity of Bt after 2 wk and because of lack of nontarget effects on the stacked near-isoline, we suggest that tissue-mediated differences, and not the presence of the Cry1Ab protein, caused the different responses among the species. Overall, our results provide evidence that adverse effects to aquatic nontarget shredders involve complex interactions arising from plant genetics and environment that cannot be ascribed to the presence of Cry1Ab proteins.