River Yamuna, in the national capital territory (NCT), commonly called Delhi (India), has been subjected to immense degradation and pollution due to the huge amount of domestic wastewater entering the river. Despite the persistent efforts in the form of the Yamuna Action Plan phase I and II (YAP) (since 1993 to date), the river quality in NCT has not improved. The restoration of river water quality has been a major challenge to the environmental managers. In the present paper, water quality index (WQI) was estimated for the River Yamuna within the NCT to study the aftereffects of the projects implemented during YAP I and II. The study was directed toward the use of WQI to describe the level of pollution in the river for a period of 10 years (2000–2009). The study also identifies the critical pollutants affecting the river water quality during its course through the city. The indices have been computed for pre-monsoon, monsoon and post-monsoon season at four locations, namely Palla, ODRB, Nizamuddin and Okhla in the river. It was found that the water quality ranged from good to marginal category at Palla and fell under poor category at all other locations. BOD, DO, total and fecal coliforms and free ammonia were found to be critical parameters for the stretch.