Salinity gradients and fluctuations can create a natural ecological filter, with few species tolerating salinity above 50 practical salinity units (PSUs). 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.