Marine microorganisms control productivity and biogeochemistry of the global ocean. In light of this fundamental importance, the Global Ocean Observing System designated microbial biomass and diversity as emerging essential ocean variables (EOV) and necessary components of an integrated and sustained ocean observing system. Long-term time series investigating marine microbial diversity are scarce, particularly in the southern hemisphere. A collaboration between the Integrated Marine Observing System (IMOS) and the Australian marine microbiology community, began sustained temporal observations of microbial dynamics in Australian waters at IMOS National Reference Stations (NRS) in 2012, leading to the establishment of the IMOS Marine Microbiome Facility in 2019. The NRS represent important marine biomes around Australia’s coastline and microbial observations from these sites allow for direct coupling of microbial diversity and function data with the full suite of biological and physicochemical measurements acquired at NRS. This data fills an important gap in our understanding of the structure and function of the pelagic organisms forming the base of marine food-webs, enabling a large diversity of research discovery and providing an unprecedented opportunity for the Australian marine science community to incorporate key microbiological parameters into important research questions. Here-in we describe some key outputs from this important collaboration.