In agriculture-dominated areas, water pollution resulting from nutrients migrating from farms to water bodies is a major concern. The migration is further exacerbated by traditional tile drain known as Uncontrolled Tile Drainage (UCTD), which removes excess water from areas to keep the water table low enough for crops to grow. UCTD, commonly used in Ontario, Canada, is believed to contribute to water quality issues, whereas Controlled Tile Drainage (CTD) is an alternative technique in which a structure controls the outlets of the drains so that water only leaves a field when the water table level exceeds a desired threshold. Considered as a Best Management Practice (BMP), CTD has been documented as an efficient practice preventing nutrients from migrating out of agricultural fields. This thesis aims to improve our understanding of the environmental benefits of replacing UCTD with CTD. Three significant contributions were achieved. The first contribution of the thesis is the improvements of the algorithm for calculating nitrates in tile flows in the Soil and Water Assessment Tool (SWAT) model. Researchers have simulated CTD by dynamically changing tile depth to mimic the operation of outlet structure gates, but it has been demonstrated that doing so results in inaccuracies, and so the algorithm in the model has been improved subsequently. The current author proposed and tested a new algorithm for calculating nitrates in tile flows that better represents the dynamics of water and nutrients in soil layers for the SWAT model. A model for the South Nation watershed, located in Ontario, Canada, was then developed and successfully calibrated using the improved SWAT model. The second contribution was the extension of the SWAT model to simulate riverine hydraulic and water quality processes by coupling it with the QUAL2Kw model. In this thesis, a procedure is developed to couple the SWAT model and the QUAL2Kw model to enable continuous simulations of 13 water quality parameters in the South Nation River system. The coupled model was calibrated and verified at various observed locations along the river during the five seasons of growth from 2006 to 2010. The simulation results suggested that CTD also improved the water quality of the river by lowering biologically available N levels of NO2--N, and NO3--N, thereby impeding phytoplankton growth in the river. The third contribution is the verification of the benefits of replacing UCTD with CTD in the future climates. The confirmation was done using the SWAT model alone, and then the coupled SWAT/QUAL2K models, using a matrix of climate change experiments performed with several Global Climate Models and Regional Climate Models. The results suggest that nutrient loading from the watershed will increase in the 2021–2050 period compared to the 1985–2006 period. Thus, pollution from agricultural fields will worsen with the current UCTD approach, while the results also show that CTD would perform effectively and stably in future climate scenarios and could counterbalance the effects of climate change on water quality. To the author’s knowledge, this study is the first attempt to date to assess the environmental effects of CTD on a watershed and river by coupling the SWAT and QUAL2Kw models. The findings expand the current scope of knowledge on the environmental effects of CTD on watersheds and rivers under current and future climate change regimes. Long periods of continuous simulation and a matrix of climate change scenarios also make this study stand out from other studies. It laid a foundation for future investigations.