Salt marsh rehabilitations have been carried out globally, with the goal of recovering structural characteristics such as diversity or abundance. Functional properties (e.g. foodwebs) are also important but less is known about the effects of rehabilitation on such factors. We investigated the benthic foodweb in a reconstructed salt marsh, which consisted of marsh vegetation and mudflats, in the artificial Shinhama Lagoon, at the head of Tokyo Bay, central Japan. We used stable carbon and nitrogen isotope analysis to assess the contributions of primary producers (marsh plants, phytoplankton, microphytobenthos and macroalgae) as nutrient sources for benthic invertebrates in vegetated and unvegetated habitats. Phytoplankton contributed to approximately 27% of the diet of benthic invertebrates and was thus the highest contributor in both habitats. In addition, marsh plants contributed about 24% of the diet of the invertebrates in vegetated habitats, and microphytobenthos contributed around 22% of the diet in unvegetated habitats. These findings are consistent with those obtained from other intact salt marshes, suggesting that the artificial Shinhama Lagoon has evolved into a natural system in terms of the benthic foodweb approximately 30 years after reconstruction. Results indicate that functional properties can be recovered by marsh restoration, and that future rehabilitation programmes should aim to recover whole ecosystems, i.e. both structural characteristics and functional properties.