Larval anurans are known for having diverse diets, but there have been relatively few studies examining their assimilation of natural foods or how they cope with variation in available resources. In our study, we estimated assimilation of food resources of two species of larval anurans that were presented with benthic substrates from a set of natural ponds. Assimilation was measured during a week-long experiment during which we renewed substrates and collected feces daily. Larvae of wood frogs (Rana sylvatica) and spring peepers (Pseudacris crucifer) were given benthic substrates from ponds shaded by deciduous forest vegetation as well as from unshaded ponds. We measured organic content in the foregut of tadpoles and from their feces. Estimates of assimilation efficiency were lower than those reported for tadpoles consuming artificial food. Both species experienced reduced assimilation efficiency on closed canopy food resources, but did not differ in their abilities to assimilate organic matter from either type of food resource. However, wood frogs processed more food during the experiment. Our results suggest that natural variation in composition of food resources among ponds could have important effects on tadpole performance and provide some support for interspecific differences in food utilization consistent with relative patterns of performance and distribution.