Despite theories of large-scale movement and assimilation of carbon in estuaries, recent evidence suggests that in some estuaries much more limited exchange occurs. We measured the fine-scale movement and assimilation of carbon by resident macroinvertebrates between adjacent saltmarsh and mangrove habitats in an Australian estuary using δ13C analysis of animals at different distances into adjacent patches of habitat. δ13C values of crabs (Parasesarma erythrodactyla −15.7 ± 0.1‰, Australoplax tridentata −14.7 ± 0.1‰) and slugs (Onchidina australis −16.2 ± 0.3‰) in saltmarsh closely matched that of the salt couch grass Sporobolus virginicus (−15.5 ± 0.1‰). In mangroves, δ13C values of crabs (P. erythrodactyla −22.0 ± 0.2‰, A. tridentata −19.2 ± 0.3‰) and slugs (−19.7 ± 0.3‰) were enriched relative to those of mangroves (−27.9 ± 0.2‰) but were more similar to those of microphytobenthos (−23.7 ± 0.3‰). The δ13C values of animals across the saltmarsh-mangrove interface fitted a sigmoidal curve, with a transition zone of rapidly changing values at the saltmarsh-mangrove boundary. The width of this transition indicated that the movement and assimilation of carbon is limited to between 5 and 7 m. The δ13C values of crabs and slugs, especially those in saltmarsh habitat, clearly indicate that the movement and assimilation of carbon between adjacent saltmarsh and mangrove habitat is restricted to just a few metres, although some contribution from unmeasured sources elsewhere in the estuary is possible. Such evidence demonstrating the extent of carbon movement and assimilation by animals in estuarine habitats is useful in determining the spatial arrangement of habitats needed in marine protected areas to capture food web processes.