Greenhouse gas (GHG; CH4, N2O) emissions from running waters are controlled by instream processes (e.g., metabolism, weathering), hydrology, channel slope, and land use types. However, little information exists on the contribution of macroinvertebrates to reach-scale GHG emissions. The invasive Asian clams (Corbicula spp.) are present in many river basins across Europe and North America, and thus their impacts on stream ecosystems are highly expected. Yet, how GHGs are regulated in situ by the clams and what conditions promote or inhibit GHG production remain poorly understood. There is evidence that methanotrophic and methanogenic symbionts present in bivalves might play a role in CH4 production and consumption. In addition, lab incubations suggested that higher nitrate (NO3-) concentration resulted in higher direct N2O emission from macroinvertebrates. Thus, we hypothesized that the scaled-up contribution from clams to stream CH4 and N2O emissions would be higher with higher NO3- concentration and greater densities of Asian clams. We conducted field microcosms in the Eno River (0.24 ± 0.11 mg/L NO3-N) and Ellerbe Creek (1.412 ± 0.031 mg/L NO3-N) in North Carolina by collecting and incubating clams in gas-tight jars. We obtained point measurements of CH4 and N2O concentrations to monitor their changes and collected water chemistry, organic matter (i.e., seston and fine benthic organic matter), discharge, and ambient dissolved gas samples. We used these data to calculate reach-scale CH4 and N2O emissions from streams and Asian clams’ contribution to GHG fluxes. Given the abundance and future expansion of the invasive Asian clams, findings from this study will improve our understanding on the ecological and biogeochemical impacts of invasive Asian clams on stream GHG emissions. This study will also provide valuable insights to inform the development of effective management and mitigation strategies for streams with high clam densities.