The prediction of nutrient pollution at realistic details is difficult due to lack of proper description of inherent processes in modelling tools. To overcome that this study has adopted a process based approach to build a semi-distributed model to simulate nutrient pollution in changing environment. The model was built to describe: (1) nutrient generation process in the catchment with consideration of different aspects of external and internal sources, (2) nutrient release from surface to the waterways via runoff and soil erosion, and (3) in-stream transport and chemical reaction process. The key novelty of this research is the linking of the nutrient generation process with transport mechanism for modelling nutrient dynamics at a basin scale. A flow capacity based approach was introduced to determine nutrient export from catchment to the waterways, which was useful to achieve the high resolution outputs from the model. The model performed reasonably well to represent the behaviour of nutrient in high flow events as well as in seasonal flow in two catchments located in distinct hydro-climatic regions. The study has shown that the nutrient model is suitable for predicting actual nutrient pollution in rivers for both high flow and seasonal flow under different hydro-climatic conditions. By simulating organic and inorganic nutrients separately, the model allows to estimate river water quality status in detail.