Bt corn is genetically-modified using genes from Bacillus thuringiensis to express Cry proteins toxic to specific pest species. After crop senescence, transgenic crop debris from Bt corn can enter waterways, exposing aquatic invertebrates that process leaf debris to Cry proteins and potentially altering ecosystem services. In particular, Cry proteins might impact the order Trichoptera as they are phylogenetically closely related to target pest species, and many play important roles in leaf processing in streams. We conducted a three-year study to examine the effect of Bt corn on headwater streams by pairing streams across five farms in Maryland, with one stream receiving Bt corn debris and the other its near-isoline non-Bt corn debris. We used a BACI (before-after-control-impact) design, with one year of sampling prior to introduction of corn tissue and two post-introduction years. We examined the aquatic invertebrate community that colonized maple and corn debris in leaf bags as well as their leaf decomposition rates in spring and fall in each stream. Minimal differences were seen between the communities, nearly all varying by stream or season throughout the study. Only one significant interaction indicated a decrease after Bt treatment, with the highest evenness in the before treatment year compared to the after treatment years. No shifts in the community were observed via Bray-Curtis ordination, and no changes in leaf decomposition rates were measured. Further, no changes in Trichoptera were measured. We conclude that Bt corn appears to have minimal risk to invertebrate communities and leaf processing in headwater streams.