The river's functional balance varies according to flow regimes and nutrient distribution. Watercourses can receive water from different point and nonpoint sources, which discharge high nitrogen load in rivers generated from domestic and industrial effluents and agricultural runoff. The excessive concentration of nitrogen load affects the riverine ecosystem by attenuating dissolved oxygen balance and disturbing the water quality. A study has been conducted to determine the nitrogen dynamics and their impact on the water quality of the Delhi stretch of Yamuna River, India, which is highly influenced by anthropogenic activities. Multivariate linear regression (MLR) was performed to gain insight into nitrogen dynamics, and structural equation modeling was applied to determine the direct (primary) and indirect (secondary) relation between the water quality parameters and the subsequent impact on water quality. Dissolved inorganic nitrogen (DIN) was measured using ammonia, nitrate, and nitrite, and total Kjeldahl nitrogen was estimated to reflect the dissolved organic nitrogen (DON). The variation in dissolved nitrogen (organic and inorganic) signifies high negative flux on the river's organic content, causing further degradation of river water quality. MLR predicted a high correlation between predicted and observed DIN at the Income Tax Office (ITO) (92.5%) and Nizamuddin (94.37%) and DON at ITO (93.49%) and Nizamuddin (95.28%). The high concentration during the lean period deteriorates the water quality tremendously and suggests that the variation in dissolved nitrogen content should be monitored carefully to maintain the river's water quality dominated by the organic load.