The weathering rate of carbonate minerals is several orders of magnitude higher than for silicate minerals. Therefore, small amounts of carbonate minerals have the potential to control the dissolved weathering loads in silicate-dominated catchments. Both weathering processes produce alkalinity under the consumption of CO2. Given that only alkalinity generation from silicate weathering is thought to be a long-term sink for CO2, a misattributed weathering source could lead to incorrect conclusions about long- and short-term CO2 fixation. In this study, we aimed to identify the weathering sources responsible for alkalinity generation and CO2 fixation across watershed scales in a degrading permafrost landscape in northern Norway, 68.7–70.5∘ N, and on a temporal scale, in a subarctic headwater catchment on the mountainside of Iskorasfjellet, characterized by sporadic permafrost and underlain mainly by silicates as the alkalinity-bearing lithology. By analyzing total alkalinity (AT) and dissolved inorganic carbon (DIC) concentrations, as well as the stable isotope signature of the latter (δ13C-DIC), in conjunction with dissolved cation and anion loads, we found that AT was almost entirely derived from weathering of the sparse carbonate minerals. We propose that in the headwater catchment the riparian zone is a hotspot area of AT generation and release due to its enhanced hydrological connectivity and that the weathering load contribution from the uphill catchment is limited by insufficient contact time of weathering agents and weatherable materials. By using stable water isotopes, it was possible to explain temporal variations in AT concentrations following a precipitation event due to surface runoff. In addition to carbonic acid, sulfuric acid, probably originating from oxidation of pyrite or reduced sulfur in wetlands or from acid deposition, is shown to be a potential corrosive reactant. An increased proportion of sulfuric acid as a potential weathering agent may have resulted in a decrease in AT. Therefore, carbonate weathering in the studied area should be considered not only as a short-term CO2 sink but also as a potential CO2 source. Finally, we found that AT increased with decreasing permafrost probability, and attributed this relation to an increased water storage capacity associated with increasing contact of weathering agent and rock surfaces and enhanced microbial activity. As both soil respiration and permafrost thaw are expected to increase with climate change, increasing the availability of weathering agents in the form of CO2 and water storage capacity, respectively, we suggest that future weathering rates and alkalinity generation will increase concomitantly in the study area.