Globally, the value of measuring and incorporating microbial diversity and community composition into environmental management plans is becoming more broadly accepted. Microbial diversity is now recognized as one of the most sensitive indicators to detect differences between disturbed and undisturbed soils in terrestrial ecosystems. However, the use of microbial indicators in the management of natural aquatic systems, both freshwater and marine, is still in development. Here, we present two case studies illustrating the way in which rapid and cost-effective measures of microbial diversity and composition (e.g. 16S rRNA amplicon sequencing) can be used for improved management in the Swan-Canning catchment of Perth, Western Australia. In the first case study, we show how the use of 16S rRNA sequencing of microbial communities across riparian soil gradients coupled with qPCR of functional genes, can be used to guide restoration and management of urban and degraded freshwater streams. In the second case study, we show how we can combine traditional seagrass health metrics (e.g. biomass and reproduction) with 16S rRNA sequencing of seagrass microbiomes to develop indicators for estuarine health. These case studies are exemplars of how an improved understanding of fundamental microbial (both free-living and host-associated) aquatic ecology (i.e. community composition) can facilitate the development of novel management and restoration strategies for aquatic systems spanning entire catchments.