A two-dimensional water quality numerical model has been developed to analyse the influence of adsorption boundary on the variation of water pollutant degradation. The characteristic finite element method is adopted to solve the discrete pollutant concentration equations, so the time-monotonicity of concentration is ensured in the convection-dominated flow field with various adsorption conditions. The second-order Runge–Kutta method is adopted to track the upstream concentration source points along the streamline, so the precision of the calculated pollutant concentration is improved even under the streamline sharp-bending condition. The flow roughness and pollutant degradation coefficient are formulated by elements according to the actual situation, so the model can quantitatively analyse the effect of various ecological restoration schemes on purification capacity in water areas. The adaptability and robustness of the model were verified by a typical engineering case, where the calculated results coincide with the measured data.