North American beaver (Castor canadensis) create impoundments that alter the physical structure of a landscape on decadal scales due to alternating dam assembly and breach events. Habitat heterogeneity of a beaver-engineered landscape through the “lifecycle” of dam establishment, failure, and succession has been recognized as source of discontinuity in headwater systems, yet formal testing of how aquatic insect basal resources vary across this temporal gradient has not been explored. Here, we investigate this gap and directly compare results from two stable isotope methods: bulk-tissue stable isotope analysis of carbon and nitrogen (BT-SIA) and compound specific stable isotope analysis of amino acids (CSIA-AA). In freshwater food web studies, essential amino acid carbon stable isotope (d13CEAA) profiles have enabled more accurate estimates of basal resource use because such profiles are generally consistent among basal resources that share broad taxonomic classification (e.g., algae, bacteria, fungi, and terrestrial plants). Therefore, we compared CSIA-AA with BT-SIA to evaluate consistency in basal resource estimates. Aquatic insects were sampled using active and passive techniques across high-energy reaches bordered by forested riparian areas (n = 24) and low-energy reaches flowing through beaver meadows (n = 21) in six headwater streams representing the temporal gradient of the beaver dam “lifecycle” and analyzed using both BT-SIA and CSIA-AA. BT-SIA results indicated that periphytic algae was the dominant basal resource assimilated to aquatic insect biomass across all site types and temporal gradients for predators (median of 58.3–95.8%), shredders (median of 83.2–94.1%), and collectors (median of 51.4–85.6%). Preliminary results from linear discriminant analysis of d13CEAA profiles show clustering of all aquatic insects with aquatic basal resources with the exception of one individual shredder, suggesting general agreement between the two methods. Results indicate CSIA-AA provides complementary validation and added resolution for detecting mixed resource pathways. For example, CSIA-AA clarified resource use of a shredder individual with multimodal BT-SIA results. Next, we will formalize these comparisons using Bayesian mixing models. This observed consistency in techniques further supports the importance of aquatic basal resources in headwater streams and suggests that this importance is consistent despite apparent beaver-driven habitat heterogeneity.