Salinity gradients and fluctuations can create a natural ecological filter, with few species tolerating salinity above 50 practical salinity units (PSU). We investigated how an inverse salinity gradient affected marine community diversity and composition in Shark Bay, a remote hypersaline coastal embayment in Western Australia. We used 16S(fish), 18S, and 16S(Bacteria) eDNA metabarcoding assays to analyse genetic sequences collected from 220 surface water samples and 216 benthic roller samples. The 44 survey sites transcended a salinity gradient of 40.1 PSU in the Eastern Gulf to 76.0 PSU in Hamelin Pool. 24,011,345 eDNA sequencing reads were detected from 5,575 operational taxonomic units (OTUs). The number of Families and OTUs, and OTUs within key Phyla, all decreased with increasing salinity, the most dramatic changes occurring over a narrow salinity range (50 - 60 PSU). However, the relative proportion of Families from each Phyla contributing to the total assemblage within each salinity range remained relatively stable. Key processes may therefore be maintained across the salinity gradient, although redundancy and resilience are compromised as diversity declines and the taxonomic composition of the communities change. Although primary producers such as cyanobacteria, seagrass and the bivalve mollusc Fragum spp. were under-represented within our data set, this may be due to a limitation of the eDNA methods used rather than their lack of presence within the ecosystem. Even with these limitations, eDNA has proven a useful tool for examining the whole marine assemblage across an inverse salinity gradient in a remote area at a broad taxonomic level.