Enhanced release of alkalinity from the seafloor, principally driven by anaerobic degradation of organic matter under low-oxygen conditions and associated secondary redox reactions, can increase the carbon dioxide (CO₂) buffering capacity of seawater and therefore oceanic CO₂ uptake. The Baltic Sea has undergone severe changes in oxygenation state and total alkalinity (TA) over the past decades. The link between these concurrent changes has not yet been investigated in detail. A recent system-wide TA budget constructed for the past 50 years using BALTSEM, a coupled physical-biogeochemical model for the whole Baltic Sea area, revealed an unknown TA source. Here we use BALTSEM in combination with observational data and one-dimensional reactive transport modelling of sedimentary processes in the Fårö Deep, a deep Baltic Sea basin, to test whether sulfate reduction coupled to iron (Fe) sulfide burial can explain the missing TA source in the Baltic Proper. We calculated that this burial can account for 26% of the missing source in this basin, with the remaining TA possibly originating from unknown river inputs or submarine groundwater discharge. We also show that temporal variability in the input of Fe to the sediments since the 1970s drives changes in sulfur burial in the Fårö Deep, suggesting that Fe availability is the ultimate limiting factor for TA generation under anoxic conditions. The implementation of projected climate change and two nutrient load scenarios for the 21st century in BALTSEM shows that reducing nutrient loads will improve deep water oxygen conditions, but at the expense of lower surface water TA concentrations, CO₂ buffering capacities and faster acidification. When these changes additionally lead to a decrease in Fe inputs to the sediment of the deep basins, anaerobic TA generation will be reduced even further, thus exacerbating acidification. This work highlights that Fe dynamics play a key role in the release of TA from sediments where Fe sulfide formation is limited by Fe availability, as exemplified for the Baltic Sea. Moreover, it demonstrates that burial of Fe sulfides should be included in TA budgets of low oxygen basins.