Deep remineralization patterns, as carbon dioxide production, were investigated in microplankton samples from several areas of eastern Mediterranean Sea. The respiration data, collected during six oceanographic surveys from 1993 through 1999, evidence biogeochemical peculiarities of the deep waters of Mediterranean as compared to the open ocean and allow drawing up an hypothesis on the possible impact of the Eastern Mediterranean Transient (EMT) on remineralization processes. The temporal trend of the oxidative processes in the basin is tightly coupled with the main features of the circulation pattern. In the Mediterranean Sea, the convective processes and the consequent advection of dense waters assume a relevant role in sustaining the amount of remineralization in the deep layers and appear to be more important than the sinking of particulate matter from the upper layers. Respiration in the deepest Mediterranean waters accounts for a greater percentage of the upper aphotic zone respiration (over 45%) than that found in the open oceans (below 21%). In addition, the increase in respiratory rates in only a few years in the Ionian Basin could represent a signal of the changes induced by the EMT, which replaced the Adriatic deepwater supply with waters of Aegean origin. The ecological change induced by the EMT, negligible in the photic layers of the eastern Mediterranean Sea, seems to concern the impact of the continental shelf pump by advection of younger, less-refractory organic matter utilizable by deep biota.