Global average temperatures and the frequency of extreme climatic events, including heat waves, are increasing due to the anthropogenic rise in greenhouse gas (GHG) emissions. Shallow aquatic areas can potentially buffer some anthropogenic alterations, acting as net sinks for nutrients and GHGs such as CO₂, CH₄ and N₂O. However, these environments are also vulnerable to climate variations, with unknown consequences for their role as climate buffers. To investigate the impact of altered temperatures on the net exchange of GHGs and nutrients, we quantified variations in net metabolism, dissolved inorganic nitrogen and GHG fluxes in sediments from the Río San Pedro creek (Bay of Cádiz) exposed to a wide range of temperatures (10 to 42 °C) over 84 hours of laboratory-controlled incubation, using core incubations, oxygen microprofiles and microbial community analysis. Sediment respiration increased significantly with temperature, with evidence of inhibition after prolonged exposure to the highest temperatures (34–42 °C), typical of heatwave conditions. Nitrogen cycling was also affected, though not straightforwardly: moderate warming increased nitrification and net nitrite efflux, while dissimilatory processes (denitrification and DNRA) appeared enhanced at higher temperatures. Key nitrification gene abundances did not increase significantly, but functional predictions from 16S rRNA gene data using PICRUSt2 indicated enrichment of the predicted denitrification pathway at the highest temperature. Although sediments were a net source of CH₄ and N₂O throughout, their temperature responses diverged: N₂O release increased up to 26–34 °C then declined, and was higher during the first days, revealing a decoupling between production and consumption over time; methane release increased exponentially with temperature throughout. Increasing heatwave frequency and duration could therefore substantially raise net CO₂ and CH₄ release from shallow coastal sediments, while N₂O responses appear more complex and non-monotonic, with uncertain net feedback on global warming.