In the oligotrophic Southeastern Mediterranean Sea (SEMS), it has been shown that dissolved inorganic nutrient (DIN) from fresh submarine groundwater discharge (FSGD) enhance primary production in coastal waters. In this study pH, Total Alkalinity (TA) and DIN of seawater and fresh water in a sea‐cave in the northern part of the Israeli Mediterranean coast and a nearby contact spring, respectively, were measured during October 2018–March 2020. The results show gradients of measured salinity, TA, pH and DIN along the cave axis year‐round, suggesting that they are influenced by FSGD. The seawater near the back of the cave was supersaturated with respect to atmospheric CO2 nearly year‐round and there is a strong positive divergence from its regional open‐water thermal dependence, which suggests that FSGD is also a source of atmospheric CO2 in this region. Comparison of TA, salinity and pCO2 from the back of the sea cave to their corresponding values from an abrasion platform monitoring site, ca. 3 km south of the cave, suggests that FSGD is occurring along the entire shoreline in this region. Thus, despite the increased productivity due to FSGD mediated nutrient enrichment of adjacent coastal waters of the oligotrophic SEMS, they are still a source of atmospheric CO2 nearly year‐round. Finally, the apparent trends of seawater acidification (ΔpH/Δt = −0.006 yrs−1) and pCO2 increase (+8 ppmV yr−1) observed at the nearby monitoring site since 2013 are explained by increased groundwater recharge and resulting FSGD total alkalinity compared to dissolved inorganic carbon inputs (ΔTA/ΔDIC = 1:1.2). Plain Language Summary Submarine groundwater discharge is an important source of dissolved inorganic nutrients that support organic matter production in the Mediterranean Sea. Furthermore, the contribution of fresh groundwater discharge to the alkalinity budget of the Mediterranean Sea compared to riverine inputs is also significant. Approximately half of the groundwater discharged into the Mediterranean originates from karst lithologies. In this study we followed the annual variations in seawater chemical properties in the Rosh‐Hanikra sea‐cave, located along the northern Mediterranean coast of Israel. The results suggest that fresh groundwater discharge supports the observed gradients of measured seawater chemistry along the cave axis year‐round with a stronger influence during the wintertime compared to summertime and that it helps maintain coastal waters as a source of atmospheric CO2 year‐round. Furthermore, the data suggest that submarine groundwater discharge, which is enriched in dissolved inorganic carbon increases the rate of ocean acidification associated with increasing atmospheric CO2 in the coastal waters of this region. Key Points Fresh submarine groundwater discharge (FSGD) is apparent in seawater properties of the Rosh‐Hanikra Mediterranean Sea sea‐cave year‐round FSGD into coastal waters in the Rosh‐Hanikra region causes them to be a source of atmospheric CO2 year‐round FSGD augments seawater acidification along the northern Mediterranean coast of Israel despite nutrient enrichment and increased productivity