Coastal ecosystems release or absorb carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O), but the net effects of these ecosystems on the radiative balance remain unknown. We compiled a dataset of observations from 738 sites from studies published between 1975 and 2020 to quantify CO2, CH4and N2O fluxes in estuaries and coastal vegetation in ten global regions. We show that the CO2-equivalent (CO2e) uptake by coastal vegetation is decreased by 23–27% due to estuarine CO2e outgassing, resulting in a global median net sink of 391 or 444 TgCO2e yr−1using the 20- or 100-year global warming potentials, respectively. Globally, total coastal CH4and N2O emissions decrease the coastal CO2sink by 9–20%. Southeast Asia, North America and Africa are critical regional hotspots of GHG sinks. Understanding these hotspots can guide our efforts to strengthen coastal CO2uptake while effectively reducing CH4and N2O emissions.