A computation scheme, which involves multi-step computation of the decoupled mass-balance equations include physical transport processes and kinetic processes in water quality models, can improve accuracy and efficiency in the numerical treatment of the kinetic processes. This paper focuses on the concept and the implementation of multi-step computation scheme in a generalized format for intratidal estuarine water quality model. The scheme is applied to the Tanshui River system using a laterally-integrated two-dimensional intratidal model. The computation efficiency of the scheme is demonstrated to promote by comparing the model results using the multi-step scheme with those using the traditional single-step explicit numerical solution of the kinetic processes. Decoupling of the mass-balance equations not only simplified the solution scheme but also makes the model flexible with respect to the additional of new state variables and to the modification of the kinetic formulation.