Summary Low-salinity polymer (LSP) flooding is a synergic emergent enhanced oil recovery (EOR) technique. Previous laboratory experiments showed noticeable improvements in displacement efficiency, polymer rheology, injectivity, and viscoelasticity. Nevertheless, when it comes to modeling LSP flooding, it is still challenging to develop a mechanistic predictive model that captures polymer-brine-rock (PBR) interactions. Therefore, this study uses a coupled MATLAB reservoir simulation toolbox (MRST)-IPhreeqc simulator to investigate the effect of water chemistry on PBR interactions during LSP flooding through varying overall salinity and the concentrations of divalent and monovalent ions. For describing the related geochemistry, the presence of polymer in the aqueous phase was considered by introducing novel solution species (Poly) to the Phreeqc database. The developed model’s parameters were validated and history matched with experimental data reported in the literature. Moreover, different injection schemes were analyzed, including low-salinity (LS) water, LSP injection (1 × LSP), and 5-times spiked LSP injection (5 × LSP) with their related effects on polymer viscosity. Results showed that polymer viscosity during LSP flooding is affected directly by Ca2+ and Mg2+ and indirectly by SO42− owing to PBR interactions on a dolomite rock-forming mineral. Monovalent ions (viz. Na+ and K+) have minor effects on polymer viscosity. Ca2+ and Mg2+ ions discharged from dolomite dissolution create polymer complexes (acrylic acid, C3H4O2) to reduce polymer viscosity significantly. The increased SO42− concentration in the injected LSP solution affects the interactions between the polymer and positively charged aqueous species, leading to minimized polymer viscosity loss. For LSP flood derisking measures, the cation’s effect was related to the charge ratio (CR). Thus, it is key to obtain an optimal CR where viscosity loss is minimal. This paper is among the few to detail the mechanistic geochemical modeling of the LSP flooding technique. The validated MRST-IPhreeqc simulator evaluates the previously overlooked effects of water chemistry on polymer viscosity during the LSP process. Using this coupled simulator, several other geochemical reactions and parameters can be assessed, including rock and injected-water compositions, injection schemes, and other polymer characteristics.