First data on microbial respiration in the Levantine Sea are reported with the aim of assessing the distribution of oxidative processes in association with the main Mediterranean water masses and the changing physical structure determined by the Eastern Mediterranean Transient. Respiratory rates, in terms of metabolic carbon dioxide production, were estimated from measured electron transport system activities in the polygonal area of the Levantine Sea (32.5–36.5 N Latitude, 26.0–30.25 E Longitude) and at Station Geo’95, in the Ionian Sea (35°34.88 N; 17°14.99 E). At the Levantine Sea, the mean carbon dioxide production rate decreased from the upper to the deeper layers and varied from 22.0±12.4 μg C h−1 m−3 in the euphotic layer to 1.30±0.5 μg C h−1 m−3 in the depth range between 1600 and 3000 m. Significant differences were found among upper, intermediate and bottom layers. The euphotic zone supported a daily carbon dioxide production of 96.6 mg C d−1 m−2 while the aphotic zone (between 200 and 3000 m) sustained a 177.1 mg C d−1 m−2 carbon dioxide production. In Station Geo’95, the carbon dioxide production rates amounted to 170.4 and 102.2 mg C d−1 m−2 in the euphotic and aphotic zones, respectively. The rates determined in the identified water masses showed a tight coupling of respiratory processes and Mediterranean circulation patterns. The increasing respiratory rates in the deep layers of the Levantine Sea are explained by the introduction of younger waters recently formed in the Aegean Sea.