Hypoxia is emerging as a major threat to marine coastal biota. Predicting its occurrence and elucidating the driving factors are essential to set successful management targets to avoid its occurrence. This study aims to elucidate the effects of warming on the likelihood of hypoxia. High-frequency dissolved oxygen measurements have been used to estimate gross primary production (GPP), net ecosystem production (NEP) and community respiration (CR) in a shallow macroalgae (Caulerpa prolifera) ecosystem in a highly human-influenced closed Mediterranean bay. Daily averaged GPP and CR ranged from 0 to 1,240.9 and 51.4 to 1,297.3 mmol O2 m−2 day−1, respectively. The higher GPP and CR were calculated for the same day, when daily averaged water temperature was 28.3 °C, and resulted in a negative NEP of −56.4 mmol O2 m−2 day−1. The ecosystem was net heterotrophic during the studied period, probably subsidized by allochthonous organic inputs from ground waters and from the surrounding town and boating activity. Oxygen dynamics and metabolic rates strongly depend on water temperature, with lower oxygen content at higher temperatures. The probability of hypoxic conditions increased at a rate of 0.39 % °C−1 (±0.14 % °C−1). Global warming will increase the likelihood of hypoxia in the bay studied, as well as in other semi-enclosed bays.