It is well known that watershed hydrology is dependent on many factors; land use, climate, and soil conditions. But the relative impacts of different types of topography and land use on the surface water are yet to be ascertained and quantified. Agriculture has been identified as a major contributor of non-point source pollution of water resources. Assessment of the environmental impact of NPS pollutants at a localized and regional scale is key component to achieve sustainable agriculture. This research attempted to use a comprehensive approach to examine the impact of land-use practices on water quality and its variation in four sub-tropical watersheds during monsoon seasons. These watersheds with different topography & land use were monitored. Surface water samples were collected daily and analyzed for nitrate nitrogen(NO3), ammonium nitrate(NH4), and total phosphate(PO4). Trends relating to seasonal changes in stream water quality as a function of land use and agricultural practices and critical hydrological processes controlling the variability of the daily water quality variables (Nitrate, Ammonia and Phosphate) in small streams were analyzed by SWAT Modelling.