The carbonate system is a vital buffering system that controls the pH of seawater and maintains a healthy environment for marine organisms. As concerns regarding the fate of anthropogenic CO2 in the oceans are rising, it is becoming increasingly urgent to systematically quantify and understand this system's parameters, particularly in heavily human-impacted areas, such as the Mediterranean Sea. To date, the paucity of time-series stations adopted to monitor the carbonate system in this sea has precluded characterizing the region at an adequate spatial resolution. Here, we present and study the seasonal and annual variability and drivers of the first carbonate system dataset collected for the Lebanese waters, monthly at the upper 80 m between 2012 and 2017 in two time-series stations offshore the North of Lebanon-Levantine Sub-basin, Eastern Mediterranean Sea. Annual trends were calculated for the non-adjusted and the adjusted carbonate system parameters (an adjustment that reduces the influence of simple-dilution-concentration [SDC] processes on the trends). Our results show high carbonate system inventory [total alkalinity (AT), total dissolved inorganic carbon (CT), and pH] compared to other Mediterranean areas. The obtained trends reflect increasing rates for both AT and CT, only significant at surface for CT (+5 ± 2 μmol kg−1.yr−1; p < 0.05). Whereas annual acidification rates were always significant (i.e. from −0.009 ± 0.004 to −0.0021 ± 0.001 pH units.yr−1 at 0 m and in the upper 80 m respectively for pHT25adj). Concomitantly, decreasing trends of the saturation states for both CaCO3 minerals were calculated (−0.1 ± 0.04 and −0.07 ± 0.02 yr−1 for calcite and aragonite respectively at surface; p < 0.05). Moreover, our results showed that SDC processes, together with CO2 release/invasion and the active overturning circulation, are controlling this system in the Lebanese seawater, Eastern-most Mediterranean Sea. Contrariwise, the increasing trend of total alkalinity, mainly attributed to SDC processes (i.e. riverine inputs, weathering during extreme events, precipitations), may be buffering the observed acidification rate, which could have been worst in case AT in our area was lower. Highlights•The first carbonate system dataset collected for the Lebanese waters, -Levantine Sub-basin, Eastern Mediterranean Sea, are presented in this study.•Our results show high carbonate system inventory compared to other Mediterranean areas with increasing rates of both AT and CT.•Annual acidification rates have been document (i.e. from −0.009 ± 0.004 to −0.0021 ± 0.001 pH units.yr−1 at 0 m and in the upper 80 m respectively for pHT25adj.•Decreasing trends of the saturation states for both CaCO3 minerals were calculated.•Simple-dilution-concentration processes, together with CO2 release/invasion and the active overturning circulation, are controlling this system in our study area.•The increasing trend of total alkalinity may be buffering the observed acidification rate, which could have been worst in case AT in our area was lower.