Pyrite existed widely in nature and its oxidative dissolution might lead groundwater to become acidic, which was harmful to the environment and indeed to artificial building materials. The reactive transport model was a useful tool to predict the extent of such pollution. However, the chemical species were coupled together in the form of a reaction term, which might lead the equations to be nonlinear and thus difficult to solve. A decoupling approach was presented: linear algebraic manipulations of the stoichiometric coefficients of the chemical reactions for the purpose of reducing the number of equation variables and simplifying the reactive source were used. Then the original and decoupled models were solved separately, by both a direct solver and an iterative solver. By comparing the solution times of two models, it was shown that the decoupling approach could enhance the computational efficiency, especially in situations using denser meshes. Using a direct solver, more solution time was saved than when using an iterative version.