Gippsland Region is a fast growing region in Victoria State of Australia. The growth has created enormous pressure on agriculture, dairy industry and other land use productivities that affects water quality of inland waters and the downstream Gippsland Lakes. Development pressure in upper catchment area and recurring extreme events of bushfire and flooding are major factors that aggravate the situation. The climate change is likely to impact further. Hence, tackling these issues has been challenging. It requires proper assessment of pollution level and prediction of future changes for decision making. For this purpose robust modelling tool is needed which is capable to describe the pollution characteristics and predict the nutrient level in changing hydro-climatic condition. With this focus this study has developed a new generation modelling tool for nutrient pollution assessment in river basin. The model has incorporated land use function and climate variability to describe nutrient generation process and linked with in-stream dynamic river model which has physical and biogeochemical process description. The developed model has been tested in other catchment for a single storm event. Now this is being applied for verification in the Latrobe River Basin for long term simulation. Further improvement has been achieved in model building. The simulation result is satisfactory with sufficient accuracy.