A good understanding has been gained about the drivers and ecological impacts of marine heatwaves (MHWs) at large and regional scales. However, studies about the impact of MHWs on estuaries are very scarce, in spite of their threat for pelagic and benthic communities. Estuaries are ecosystems with high productivity and biodiversity that sustain activities like aquaculture and fisheries. Some negative impacts of MHWs in estuaries have been associated with the proliferation of harmful algal blooms, kelps dieback, increased prevalence of oyster disease and abalone mortality, as well as poor performance in farmed salmon. As remote sensing and climate models are not suitable, field observations and higher resolution numerical models are more appropriate to study the impact of MHWs in coastal areas, estuaries, and the land-sea interface. This study combines model outputs with observations to investigate how MHWs impact in oceanographic characteristics of estuaries, using the Huon Estuary (Tasmania, Australia) as a study case. Results show that, depending on the advective- or air-sea heat flux driven MHWs, the temperature distribution, vertical mixing, horizontal circulation and stratification can show anomalous patterns, also connected with the river and wind anomalous variation.