The study illustrates the utility of STREAM II as a modeling package to determine the pollution load due to organic matter in the River Yamuna during its course through the National Capital Territory that is Delhi, India. The study was done for a period from 1995-2005. Model simulates the dissolved oxygen and biochemical oxygen demand parameters in a two-dimensional fashion by performing the numerical solution to a set of differential equations representing aquatic life with the help of Crank-Nicholson finite difference method. The model was simulated and calibrated through the field water-quality primary data and the secondary data which were taken from Central Pollution Control Board. The main reasons for the high river pollution is increasing population of Delhi and other states, leading to generation of huge amounts of domestic sewage into the river Yamuna. The model gave a good agreement between calibrated and observed data, thus, actualizing the validity of the model. However, discrepancies noticed during model calibrations were attributed to the assumptions adopted in the model formulation and to lack of field data.