Estuaries are diverse ecosystems vital to land-ocean connectivity; and yet until now, we have lacked information on their response to climate change. We present data on climate change in Australian estuaries over twelve-years, spanning >1500 kilometres of the Australian coastline. We also investigate how this change may affect oyster aquaculture. From 2007- 2019, We found estuaries to have warmed by 2.16oC on average, at a rate of 0.2°C year-1, with waters acidifying at a rate of 0.09 pH units. These changes are an order of magnitude faster than predicted by global models. Importantly, the response of estuaries is dependent on their morphology and catchment development; lagoons, followed by rivers, are warming and acidifying the fastest due to high surface-area to volume ratios and low oceanic exchange. Warming and acidification in estuaries, spanning several bioregions, indicates change on a continental scale, and of a magnitude that is likely to affect the physiological and microbial function of oysters. Manipulative experiments exposing oysters to elevated temperatures (+ 4 °C) and acidification (pH 7.8) have demonstrated increased metabolic rates, decreased extracellular pH and increases in potentially pathogenic bacteria. Taken together, these findings show an urgent need to protect estuaries and the industries they support.