The effects of short-term heatwave extremes on biogeochemical cycling and fluxes in a temperate estuary of a semi-dry climate were studied using an experimental setup of temperature-controlled benthic incubations. The results demonstrated a strong thermal effect, notably under extreme warming events, for shifts in exchanges across the sediment-water interface. Extreme heatwave conditions (+5 °C of the seasonal mean) boosted acidification, hypoxia, and ammonification, due to accelerated remineralization rates, resulting in strong effluxes of NH₄, Si(OH)₄, and PO₄ to the overlying water. These excessive nutrient loads may increase eutrophication risk via runoff or tidal action, specifically in adjacent oligotrophic coastal waters. CO₂ production rates reached ~4000 µatm under extreme hypoxia and acidification, 2.3-fold higher than the ambient rate, with a maximal flux of ~27.0 mmol m-2 d-1. Hence, our experiments show that marine heatwaves amplify CO₂ emissions while reducing the CO₂ buffering capacity of temperate estuaries. It emphasizes temperate estuaries as highly sensitive ecosystems to climate change.