In the present study, long-term spatio-temporal variability in runoff coefficient (C) for different drainage areas of Upper Tapi basin, India, is analysed. The Upper Tapi basin is divided into two sub-catchments, Burhanpur and Purna, which are contrasting in nature in terms of their physiographic and climatic characteristics. The digital filter algorithm has been used to separate the base flow from observed streamflow for respective drainage areas. The sensitivity of the parameters involved in base flow separation is assessed by incorporating the hydrological and hydrogeological properties of individual drainage areas. The C values are then computed at different temporal scales, namely, daily, monthly, seasonal and annual, for different drainage areas. The effects of physiographic features such as topography, geology, soil type, and land use; and climatic features such as rainfall, temperature, and evapotranspiration, on the variability of C values are further investigated. The analyses reveal that Burhanpur sub-catchment (C = 0.39) yields higher C value compared to Purna sub-catchment (C = 0.11) at annual time scale. The C values clearly highlight the diversity in response of both sub-catchments, due to their distinct physiographic and climatic characteristics, and enabled us to study the variability in annual water balance of the basin.