Seagrass meadows are among the most productive ecosystems on Earth, providing nursery habitats that enhance biodiversity and fisheries production. Loss of seagrass ecosystems globally are placing these important functions at risk. Seagrass habitats in Trinity Inlet, Cairns have been monitored annually since 2001, where previously a fisheries monitoring programme was present in its seagrass meadows from the 1980’s to the early 2000’s. Several years of La Niña climate patterns producing high rainfall and a series of tropical cyclones, led to the almost complete disappearance of previously persistent seagrass meadows in Trinity Inlet. This created a valuable opportunity for a renewed sampling effort, where seagrass meadows were previously persistent, to determine the ecological change in juvenile fish and prawn assemblages against historical baselines. Results showed significant reductions in fish abundance and species richness, and a marked decline in abundance of a major commercial prawn species. Since 2016, there has been a rapid recovery of the seagrass meadow, with the total seagrass area reaching values above the long term average. From 2023, we conducted assessments of sites where seagrass has since recovered, utilising eDNA metabarcoding with traditional beam-trawling surveys as a possible method for future fish and prawn assessments in seagrass habitats.