A new grid-based model of nutrient dynamics and transport process has been developed within a distributed hydrological modelling framework and integrated with river network module. The key aspect of this development is a process based description of nutrient generation process on the land surface and its related nutrient release with hydrologic runoff and soil erosion. Whereas the conventional modelling uses the event mean concentration method for nutrient dynamics modelling and estimates nutrient loads from catchments to the rivers this study has introduced an export function based release related with flow capacity. The river module solves the dynamic equation for transport and chemical reaction. The model output is available in high spatial and temporal resolution, which was tested and verified applying in two catchment areas from different hydro-climatic backgrounds. The model was able to simulate short term high intensity flood events as well as long term seasonal patterns. The simulated results for most of the nutrient parameters are within acceptable range as reflected by measures of statistical indices and visual interpretation. For example, the R2 values for different nutrient levels in the Saru River, Japan are within the range of 0.83–0.99 and 0.66–0.87 for calibration and validation, respectively. Similarly, the relative root mean square error (RRMSE) values for different nutrient levels in the Saru River range between 0.06–0.22 and 0.06–0.26 for calibration and validations, respectively. The maximum load of nutrients in each grid was extracted from time series output, analyzed further and presented in two dimensional maps, which showcase the usefulness of the model in decision making process for management of land and maintenance of the in-stream water quality.