Hydrogen isotopes (δ2H) are often used to infer the origins of migratory animals based on the strong correlation between deuterium content of tissues and long-term patterns of precipitation. However, the extreme flood and drought dynamics of surface waters in prairie wetland systems could mask these expected correlations. We investigated H isotopic variability in an aquatic food web associated with Tree Swallows (Tachycineta bicolor) that rely heavily on wetland-derived aerial insects for food. We evaluated isotopic turnover and incorporation of environmental water into tissue, processes that could affect H isotopic composition. Wetland water and aquatic invertebrates showed intra- and interannual H isotopic variation mainly related to evaporation and the amount and timing of precipitation. Snails showed rapid turnover of tissue deuterium and a large contribution of environmental water to their tissues. Swallow feather deuterium (δ2Hf) was variable but did not clearly follow changes in any of the food web compartments measured. Instead, isotopic variability may have been driven by shifts in the type or relative amounts of prey consumed and types of wetlands used. Nevertheless, despite relatively high variance in δ2Hf, the majority of birds fell within the predicted range of δ2Hf for the study area, revealing that significant trophic averaging occurred. However, both (presumed) diet shifts and variable hydrological conditions have the potential to greatly increase variance that must be considered when assigning origins of migratory animals based on δ2H.