Estuary temperatures increased by 2.16 °C on average over 12 years, at a rate of 0.2 °C year−1, with waters acidifying at a rate of 0.09 pH units and freshening at 0.086 PSU year−1. The response of estuaries to climate change is dependent on their morphology. Lagoons and rivers are warming and acidifying at the fastest rate because of shallow average depths and limited oceanic exchange. The changes measured are an order of magnitude faster than predicted by global ocean and atmospheric models, indicating that existing global models may not be useful to predict change in estuaries.