As the planted acreage of genetically-modified crops increases annually around the world, so will the debris entering waterways containing plant incorporated protectants (PIPs). Valued for their high specificity and low impact on the environment, the activity and impact of crop PIPs on non-target terrestrial organisms are studied thoroughly. However, these parameters are relatively unexplored in flowing water systems. Since headwater streams near agricultural areas tend to have lower input, storage, and transport of organic matter, windblown crop debris may provide a disproportionately high source of allochthonous energy and nutrients for the biota. In this study we examined the sublethal growth effects of PIP delta endotoxins Cry1Ab and Cry3Bb from Bacillus thuringiensis var. kurstaki expressed in corn tissue on non-target stream invertebrates in the laboratory. Four different invertebrate shredder taxa (Asselidae, Lepidostomatidae, Limnephilidae, Tipulidae) were collected from the field and monitored for sub-lethal responses to three corn isolines: a non-Bt hybrid, a hybrid expressing the Cry1Ab toxin, and a stacked hybrid expressing both the Cry1Ab and Cry3Bb toxins. Three of the four taxa exhibited a significant decrease in specific growth metrics when fed Bt-corn compared with the non-Bt control isoline. The potential ecological implications of the sublethal responses are discussed.