The chemistry of the pore fluid within clayey sediments frequently changes in various processes. However, the impacts of pore fluid chemistry have not been well included in the hydraulic permeability model, and the physical bases behind the salinity sensitivity of the hydraulic permeability remains elusive. In this study, a theoretical model for the hydraulic permeability of clayey sediments is proposed, and impacts of the pore fluid chemistry are quantitatively considered by introducing electrokinetic flow theory. Available experimental data were used to verify the theoretical model, and the verified model was further applied as a sensitivity analysis tool to explore more deeply how hydraulic permeability depends on pore fluid chemistry under different conditions. Coupling effects of pore water desalination and the effective stress enhancement on the hydraulic permeability of marine sediments surrounding a depressurization wellbore during hydrate production are discussed. Results and discussion show that the hydraulic permeability reduction is significant only when the electric double layer thickness is comparable to the characteristic pore size, and the reduction becomes more obvious when the ion mobility of the saline solution is smaller and the surface dielectric potential of clay minerals is lower. During gas hydrate production in the ocean, the salinity sensitivity of the hydraulic permeability could become either stronger and weaker, depending on whether the original characteristic pore size of marine sediments is relatively large or small.