Seagrass meadows are among the most productive ecosystems on earth providing nursery habitats that enhance biodiversity and fisheries production. Loss of seagrass ecosystems globally is placing these important functions at risk. Several years of La Nińa climate patterns, producing high rainfall events and a series of tropical cyclones, led to almost complete disappearance of previously enduring seagrass meadows in Trinity Inlet, Cairns with limited recovery over a four-year period. Trinity Inlet had a fisheries monitoring program in its seagrass meadows from the 1980’s to the early 2000’s, making it one of the most studied estuaries in northern Australia. The loss of seagrass created a valuable opportunity of renewed sampling where seagrass meadows previously existed to determine the ecological change in juvenile fish and prawn assemblages against historical baselines. Results showed significant reductions in fish abundance and species richness following seagrass declines and a marked decline in abundance of a major commercial prawn species. In 2023, we will be conducting assessments of sites where seagrass has since recovered, utilising eDNA techniques with traditional beam-trawling surveys as a possible method for future fish assessments in seagrass habitats. This study highlights the ecological and economic consequences of seagrass loss in tropical estuaries.