Abstract Salt marshes, which sustain high productivity, serve as essential living environments for a wide range of organisms. The aquatic food web in salt marshes is basically supported by the high primary production of aquatic algae within the intertidal zone and the organic matter contributed from the terrestrial ecosystems, including the adjacent supratidal zone. As salt marshes facilitate the incorporation of terrestrially fixed energy into estuarine and marine food webs, they represent a key environment for understanding energy transfer from land to marine ecosystems. However, the energy contribution from terrestrial ecosystems to salt marsh food webs remains unquantified. Stable isotope ratios of carbon (δ 13 C) and nitrogen (δ 15 N) recorded in organisms have been widely used for identifying dietary carbon and nitrogen sources in food webs and for estimating trophic positions (TPs). Compound-specific isotope analysis (CSIA) of nitrogen within amino acids (AAs) provides a highly precise approach for identifying the dietary nitrogen sources and TPs. The δ 15 N values of phenylalanine (δ 15 N Phe ) in organisms reflect those in their diets, while differences in the δ 15 N values between glutamic acid (δ 15 N Glu ) and phenylalanine (Δ 15 N Glu-Phe ) reflect the TP of the organism (TP Glu/Phe ). Since the conversion from Δ 15 N Glu-Phe to TP Glu/Phe varies depending on the contribution of nitrogen from vascular plants, comparing the ecologically estimated TP value (TP est ), assigned based on feeding ecology, with TP Glu/Phe allows for the back-calculation of the dietary nitrogen contribution from terrestrial ecosystems sustained by vascular plants. In this study, we analyzed δ 13 C and δ 15 N, in particular, conducted CSIA of nitrogen within AAs in animals inhabiting the salt marsh of the Obitsu River estuary located in Tokyo Bay. The results showed that bulk δ 13 C ranged from − 25.1 to − 13.9‰ and δ 15 N Phe from 3.8 to 10.2‰, indicating that both aquatic algae and terrestrial vascular plants serve as ultimate dietary carbon and nitrogen sources. Furthermore, the comparison between TP Glu/Phe and TP est clearly demonstrated a substantial nitrogen contribution from terrestrial ecosystems to various salt marsh animals, and the overall dietary nitrogen contribution was estimated to be at least 30%. This study demonstrates the advantages of CSIA of nitrogen within AAs in elucidating the complex salt marsh food webs.