Studies in recent years have shown that most reactive pollutants in natural rivers originate from non-point sources such as agricultural lands and informal settlements through rainfall runoff. Much work has centred on simulating decaying substances in rivers from point-source discharges. To expand on the area of non-point source modelling in rivers, a non-point source hybrid cells in series model for simulation of reactive pollutants in rivers is proposed. The potential of the proposed model has been demonstrated and found to simulate decay from non-point sources in streams and rivers satisfactorily. The proposed model is compared with the numerical solution of the ADE model with added components for non-point source and first-order reaction kinetic. The comparisons indicate reasonably good agreement. The breakthrough curves obtained from the proposed model shows its capability to simulate reactive pollutant transport in natural rivers effectively.