Plankton form the base of the marine food web and are sensitive indicators of ecosystem health and global change. Biogeochemical, ecosystem and size-based models show that plankton play a pivotal role in ecosystem dynamics, fishery productivity and system resilience. Here we describe several sensitive indicators to assess ecosystem change utilising biodiversity, biomass, and size spectra data. The indicators were developed using plankton data from Australia’s two Integrated Marine Observing System (IMOS) long-term monitoring plankton surveys: the seven National Reference Stations, and the Australian Continuous Plankton Recorder (AusCPR) survey, integrated with biogeochemical and physical parameters from other IMOS data sources. The indicators presented include: an index of the strength of the East Australian Current based on thermal preferences of the copepod community; a multivariate index describing the degree that ocean acidification might be impacting calcifying zooplankton; and an assessment of the impact of climate change on plankton based on the Community Temperature Index. The diversity of plankton indicators showcased here highlight the importance of the IMOS plankton dataset and its power in describing the state and trends of lower trophic levels in Australia’s marine ecosystems.