Abstract. A combination of elemental analysis and stable isotope analysis (SIA) was used to assess and monitor C, N and S cycling of a mangrove ecosystem that suffered mass dieback of trees in the Gulf of Carpentaria, Australia in 2015–16, attributed to an extreme drought event. Three field campaigns were conducted over a period from 2016 to 2018, at 8, 20 and 32 months after the event. Samples including invertebrates, mangroves, and sediment were analysed for CNS elemental and isotopic compositions including compound-specific stable isotope analysis (CSIA) of amino acid carbon. Samples collected from the impacted ecosystem were enriched in 13C, 15N and 34S relative to those from an adjacent unimpacted reference ecosystem, likely indicating lower mangrove carbon fixation, lower nitrogen fixation and lower sulfate reduction in the impacted ecosystem. For example, invertebrates representing the feeding types of grazing, leaf feeding, and algae feeding were more 13C enriched at the impacted site, by 1.7–4.1 ‰ and these differences did not change over the period from 2016 to 2018. The CSIA data indicated widespread 13C enrichment across five essential amino acids and all groups sampled (except filter feeders) within the impacted site. Mangrove seedling and sapling populations increased substantially from 2016 to 2018 in the impacted forest, suggesting recovery of the mangrove vegetation. Recovery of CNS cycling, however, was not evident even after 32 months, suggesting a biogeochemical legacy of the mortality event. Continued monitoring of the post-dieback forest would help to predict the long-term trajectory of ecosystem recovery. In such long-term monitoring programs, SIA that can track biogeochemical changes over time can help to detect underlying biological mechanisms that drive changes and recovery of the mangrove ecosystem. To gain further insight, our use of CSIA can help show feeding dependencies in mangrove food webs and their response to disturbances.