This study aimed to identify the factors responsible for the major ion composition of pore water from the bottom sediments of the Bratsk water reservoir, which is part of the largest freshwater Baikal-Angara water system. In the Bratsk reservoir, the overlying water was characterized as HCO3–Ca–Mg type with the mineralization ranging between 101.2 and 127.7 mg L−1 and pore water was characterized as HCO3–SO4–Ca, SO4–Cl–Ca–Mg and mixed water types, which had mineralization varying from 165.9 to 4608.1 mg L−1. The ionic composition of pore waters varied both along the sediment depth profile and across the water area. In pore water, the difference between the highest and lowest values was remarkably large: 5.1 times for K+, 13 times for Mg2+, 16 times for HCO3−, 20 times for Ca2+, 23 times for Na+, 80 times for SO42−, 105 times for Cl−. Such variability at different sites of the reservoir was due to the interrelation between major ion concentrations in the pore water and environmental parameters. The major factor responsible for pore water chemistry was the dissolution of sediment-forming material coming from various geochemical provinces. In the south part of the reservoir, Cl−, Na+ and SO42− concentrations may significantly increase in pore water due to the effect of subaqueous flow of highly mineralized groundwater.