Determining the effects of species loss on ecosystems has received considerable attention given the current threats many ecosystems are facing. A significant body of research has yielded many insights to this question, but this work has been limited by a focus on ecosystems where primary production plays a significant role in energy transfer. As many ecosystems rely on energy sources that are not derived from in situ production, there is a need to better understand how species loss will affect ecosystems of varying trophic states. To examine the effects of species loss on an ecosystem that is not reliant on in situ primary production, we manipulated the larval amphibian community of temporary forest ponds. These ponds are heterotrophic systems that rely on allochthonous inputs of detritus as a basal energy source. The larvae of two amphibian species that are prone to local extinction, wood frogs (Lithobates sylvatica) and spotted salamanders (Ambystoma maculatum), were removed from ponds and net ecosystem production was monitored. We found no effects of the removal of these top consumers on ecosystem functioning or on lower trophic groups (i.e., zooplankton, algae, bacteria). While amphibians can influence food web dynamics in other systems, their influence on system processes in temporary forest ponds appears to be limited. We hypothesize that the lack of any effects is due to the microbial degradation of detritus “swamping” the system, providing more than enough energy to maintain the food web, and/or due to omnivory dampening species interactions. These data indicate that the functioning of heterotrophic systems may be inherently stable due to internal dynamics that minimize interaction strengths among trophic groups.