The amount and intensity of runoff at catchment scale are largely determined by the presence of impervious land cover types, which are predominant in an urbanized area. This paper examines the impact of different methods for estimating impervious surface cover on the prediction of peak discharges as determined by a fully distributed rainfall-runoff model (WetSpa). The study of River Yamuna and Hindon basin area shows detailed information on the spatial distribution of impervious surfaces, as obtained/calibrated from remotely sensed data. It produces substantial estimates of peak discharges for different types of urban land uses. Land use and cover change in Noida during 1981–2011 and historical hydrological data during 1957–2010 have been used to determine the results. It shows that the direct runoff from urban areas is responsible for a flood event compared with runoff from other land use areas. The interflow from forested, pasture and agricultural field areas contributes to the recession flow. The study also demonstrates that sub-pixel estimation of imperviousness may be a useful alternative for more expensive high-resolution mapping for rainfall-runoff modeling at small scale based on pre-existing land use pattern and the two flooding scenarios. The study proves that rapid urbanization has resulted in losses of farmland, forest and shrub since 1995 as more than 36% of the forest and 22% of the shrub areas were transformed into farmlands and settlements. The changed hydrological condition has impaired the river's flood protection capacity. Apart from natural processes, human activities driven by socio-economic transformation are being considered as a major driver for the increasing flood risks.