Microbes are the most ancient, the most phylogenetically diverse and most widespread life form on Earth occupying every conceivable niche, driving key ecosystem processes in natural, managed and engineered environments and therefore, intrinsically linked to ecosystem state. The fundamental importance of microbes for ecosystem function, environmental prevalence, sensitivity to environmental changes, and rapid replication rates, all point to the likelihood that microbial communities could offer an earlier indication of ecosystem changes compared to traditional bioindicators. Yet, aside from pathogen monitoring (e.g., food, water, agriculture, clinical), the uptake and implementation of microbiome-based insights in routine biomonitoring has been slow. There are several reasons for this, including the difficulty of distilling large and complex datasets into meaningful metrics for non-specialist end-users, the validation of these metrics within existing regulatory frameworks, and the absence of pathways to implement these metrics into management processes. We tested the broad applicability of a microbial community-based index, the microgAMBI1, at 36 estuarine sites around Australia. The locations represent a range of biogeochemical conditions, geography, land use and catchment characteristics subject to differing types and levels of anthropogenic pressure and include a variety of survey designs that encompass spatial, temporal and experimental comparisons.