Long-term determination of carbon dioxide data is a priority requirement to ensure a realistic picture of how ocean seawater properties change as the result of atmospheric evolution. Due to the extreme daily and seasonal variability of the carbonate system characteristics, constant autonomous measurements are a necessity when seeking to provide total spatial–temporal coverage of inorganic carbon data. We present here results of a one-year study in the Eastern Mediterranean Aegean Sea by using a new spectrophotometric pH-based system, applicable in long time deployments. The manifold has proved to be capable of providing sea-surface temperature and salinity together with highly accurate pH values determined each 6h over the period between September 2013 and October 2014. The average seasonal temperature difference of 12.4°C, determined from March to September, can be correlated to the seasonal pH decrease of 0.2pH units, from 8.18 to 7.98. The area also presented a maximum seasonal change in partial pressure of CO2 of 208μatm, computed from the salinity-based total alkalinity values. The Saronikos area in the Aegean Sea was characterized to be a thermodynamically controlled region, since it is oligotrophic, acting as a source of CO2 into the atmosphere of 0.20molm−2yr−1.