Saline and hypersaline wetlands account for almost half of the volume of inland water globally. They provide pivotal habitat for a vast range of species, including crucial ecosystem services for humans such as carbon sink storage and extractive resource reservoirs. Despite their importance, effective ecological assessment is in its infancy compared to current conventional surveys carried out in freshwater ecosystems. The integration of environmental DNA (eDNA) analysis and traditional techniques has the potential to transform biomonitoring processes, particularly in remote and understudied saline environments. In this context, this preliminary study aims to explore the potential of eDNA coupled with conventional approaches by targeting five hypersaline lakes at Rottnest Island (Wadjemup) in Western Australia. We focused on the invertebrate community, a widely accepted key ecological indicator to assess the conservational status in rivers and lakes. The combination of metabarcoding with morphology-based taxonomic analysis described 16 taxa belonging to the orders Anostraca, Diptera, Isopoda, and Coleoptera. DNA-based diversity assessment revealed more taxa at higher taxonomic resolution than the morphology-based taxonomic analysis. However, certain taxa (i.e., Ephydridae, Stratyiomidae, Ceratopogonidae) were only identified via net surveying. Overall, our results indicate that great potential resides in combining conventional net-based surveys with novel eDNA approaches in saline and hypersaline lakes. Indeed, urgent and effective conservational frameworks are required to contrast the enormous pressure that these ecosystems are increasingly facing. Further investigations at larger spatial-temporal scales will allow consolidation of robust, reliable, and affordable biomonitoring frameworks in the underexplored world of saline wetlands.