The build-up of sulphide concentrations in sediments, resulting from high inputs of organic matter and the mineralization through sulphate reduction, can be lethal to the benthos. Sulphate reduction is temperature dependent, thus global warming may contribute to even higher sulphide concentrations and benthos mortality. The seagrass Posidonia oceanica is very sensitive to sulphide stress. Hence, if concentrations build up with global warming, this key Mediterranean species could be seriously endangered. An 8-year monitoring of daily seawater temperature, the sulphur isotopic signatures of water (δ34Swater), sediment (δ34SCRS) and P. oceanica leaf tissue (δ34Sleaves), along with total sulphur in leaves (TSleaves) and annual net population growth along the coast of the Balearic archipelago (Western Mediterranean) allowed us to determine if warming triggers P. oceanica sulphide stress and constrains seagrass survival. From the isotopic S signatures, we estimated sulphide intrusion into the leaves (Fsulphide) and sulphur incorporation into the leaves from sedimentary sulphides (SSleaves). We observed lower δ34Sleaves, higher Fsulphide and SSleaves coinciding with a 6-year period when two heat waves were recorded. Warming triggered sulphide stress as evidenced by the negative temperature dependence of δ34Sleaves and the positive one of Fsulphide, TSleaves and SSleaves. Lower P. oceanica net population growth rates were directly related to higher contents of TSleaves. At equivalent annual maximum sea surface water temperature (SSTmax), deep meadows were less affected by sulphide intrusion than shallow ones. Thus, water depth acts as a protecting mechanism against sulphide intrusion. However, water depth would be insufficient to buffer seagrass sulphide stress triggered by Mediterranean seawater summer temperatures projected for the end of the 21st century even under scenarios of moderate greenhouse gas emissions, A1B. Mediterranean warming, therefore, is expected to enhance P. oceanica sulphide stress, and thus compromise the survival of this key habitat along its entire depth distribution range. © 2013 John Wiley & Sons Ltd.