Abstract. Deep coastal inlets are sites of high sedimentation and organic carbon deposition that account for 11 % of the world's organic carbon burial. Australasia's mid- to high-latitude regions have many such systems. It is important to understand the role of climate forcings in influencing hypoxia and organic matter cycling in these systems, but many such systems, especially in Australasia, remain poorly described. We analysed a decade of in situ water quality data from Macquarie Harbour, Tasmania, a deep coastal inlet with more than 180 000 t of organic carbon loading per annum. Monthly dissolved oxygen, total Kjeldahl nitrogen, dissolved organic carbon, and dissolved inorganic nitrogen concentrations were significantly affected by rainfall patterns. Increased rainfall was correlated to higher organic carbon and nitrogen loading, lower oxygen concentrations in deep basins, and greater oxygen concentrations in surface waters. Most notably, the Southern Annular Mode (SAM) significantly influenced oxygen distribution in the system. High river flow (associated with low SAM index values) impedes deep water renewal as the primary mechanism driving basin water hypoxia. Climate forecasting predicts increased winter rainfall and decreased summer rainfall, which may further exacerbate hypoxia in this system. Currently, Macquarie Harbour's basins experience frequent (up to 36 % of the time) and prolonged (up to 2 years) oxygen-poor conditions that may promote greenhouse gas (CH4, N2O) production altering the processing of organic matter entering the system. The increased winter rainfall predicted for the area will likely promote the increased spread and duration of hypoxia in the basins. Further understanding of these systems and how they respond to climate change will improve our estimates of future organic matter cycling (burial vs. export).