Understanding the resilience of aquatic ecosystems to climate and human impacts requires a long term perspective that is rarely attainable via contemporary monitoring programmes. Ecosystem management of the Coorong Lagoon in South Australia, for example, is based on limited knowledge of its natural variability. One solution to this challenge can be found in measuring the elemental and isotopic composition of bivalve shells isolated from sediment cores. The analyses provide quantitative estimates of past temperature and water chemistry on timescales ranging from months to millennia. The micromollusc Arthritica helmsi is abundant in the modern Coorong ecosystem and well preserved in sediments, and can thus provide an opportunity to assess sub-annual change through time. Synchronous monitoring of A. helmsi and the waters in which they live was undertaken to provide a modern calibration between the geochemical signals in the shells and physical and chemical water properties. Oxygen isotopes as well as trace elemental ratios (e.g. Sr/Ca, Mg/Ca, Ba/Ca) were measured in modern shells and waters collected periodically over 18 months, alongside water temperature, pH and salinity. Micron-scale geochemical transects were analysed on individual shells using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to determine sub-annual scale variations in water chemistry. These data were combined with bulk shell stable isotope measurements, which record conditions during the lifetime of the individual. Trace elemental ratios display a relationship with temperature in modern shells, while oxygen isotope ratios reveal a relationship with salinity as a function of water mass mixing and evaporation. These modern calibrations were applied to shells from a core spanning the last 2500 years to produce a record of past environmental change in the South Lagoon of the Coorong. This long term perspective will strengthen our understanding of this complex ecosystem and aid in placing modern conditions into context.