The River Kali in western Uttar Pradesh, India is a typical water course for untreated municipal and industrial effluents. The river receives considerable amounts of waste every day from the industries and municipal area of Muzaffarnagar town. Agricultural runoff is the other major factor in pollution of the river water. The mass balance calculations conducted on the river reach indicate that nitrate and phosphate from the non-point sources constitute 32.4 and 11.2% of the total load, respectively. The resulting differential loading, if adjusted for uncharacterized non-point contribution to the load, may represent the total point sources load to the river minus any losses due to volatilization, settling, and/or degradation. Indirect monitoring using upstream/downstream sampling locations provides a viable alternative to conventional methods for measuring the changes in the concentration and/or load to the river.