The spatial variability in hydrography (salinity and temperature) and carbonate chemistry (alkalinity - AT, total inorganic carbon concentration - CT, pH, CO2 partial pressure - pCO2, and the saturation state of aragonite - ΩAr) in high meltwater season (summer) was investigated in four Spitsbergen fjords - Krossfjorden, Kongsfjorden, Isfjorden, and Hornsund. It was found that the differences in hydrology entail spatial changes in the CO2 system structure. AT decline with decreasing salinity was evident, hence it is clear that freshwater input generally has a diluting effect and lowers AT in the surface waters of the Spitsbergen fjords. Significant surface water AT variability (1889–2261 µmol kg−1) reveals the complexity of the fjords’ systems with multiple freshwater sources having different alkalinity end-member characteristics and identifies the mean AT freshwater end-member of 595 ± 84 µmol kg−1 for the entire region. The effect of AT fluxes from sediments on the bottom water was rather insignificant, despite high AT values (2288–2666 μmol kg−1) observed in the pore waters. Low pCO2 results in surface water (200–295 μatm) points to intensive biological production, which can strongly affect the CT values, however, is less important for shaping alkalinity. It has also been shown that the freshening of the surface water in the fjords reduces significantly ΩAr (an increase in freshwater fraction contribution by 1% causes a decrease in ΩAr by 0.022). Although during the polar day, due to low pCO2, ΩAr values are still rather far from 1 (they ranged from 1.4 to 2.5), during polar night, when pCO2 values are much higher, ΩAr may drop markedly. This study highlights that the use of salinity to estimate the potential alkalinity can carry a high uncertainty, while good recognition of the surface water AT variability and its freshwater end-members is key to predict marine CO2 system changes along with the ongoing freshening of fjords waters due to climate warming.