This paper is focused on the monitoring of the diffuse pollution characteristics from the agricultural land confining the River Yamuna in Delhi (capital of India). Agricultural fields surrounding the Yamuna river are direct nonpoint source of pollution impacting the river quality. The study includes watershed delineation for the River Yamuna using SWAT (2005) and land use classification for the city using GIS and remote sensing. Thereafter, the rainfall-runoff pollutant concentrations from the mixed agricultural land use were assessed for the 2006 and 2007 monsoon period (July–September). Runoff was measured using SCS method and grab samples of rainfall runoff were collected at three stations namely Old Delhi Railway Bridge (ODRB), Nizamuddin and Okhla bridge in Delhi. The samples were analysed for physico-chemical and biological parameters. Rainfall runoff and event mean concentrations (EMCs) for different water quality parameters were characterized and the effect of land use was analyzed. The average EMCs for BOD, COD, ammonia, nitrate, TKN, hardness, TDS, TSS, chlorides, sulfates, phosphate, fluorides and TC were 21.82 mg/L, 73.48 mg/L, 72.68 μg/L, 229.87 μg/L, 15.32 μg/L, 11.36 mg/L, 117.44 mg/L, 77.60 mg/L, 117.64 mg/L, 135.82 mg/L, 0.08 mg/L, 0.85 mg/L and 2,827.47 MPN/100 mL, respectively. The EMCs of TSS, nitrogen and its compounds, phosphate and BOD were high.