Traditional techniques in surface water balance computations revolve around point-based observed results of climatic variables. Basin-wide areal estimates derived from point interpolations may not reflect true character of sub-regional variations. Hence, pixel-wise water balance computation in the case of lower Yamuna river basin falling under Himalayan river system of India, is attempted in this paper using remote sensing and Geographical Information System based approach. A comparison of point and area-based estimates has been done based on both Thornthwaite and Penman methods. Water balance computations, aridity, humidity and moisture indices, surplus and deficit values at given data points have been used in map-based calculations by developing a script in GIS software – ILWIS (Integrated Land Water Information System). It was found that water balance computations, using point-based rainfall and other climatological data, result into broad generalization of deficit and surplus zones around meteorological stations. But, when zonal landuse and soil maps are crossed in GIS environment, then pixel-wise calculations of available water capacity can be used along with isohyetal maps to produce better areal estimates of hydrological regions. The results of pixel-wise computations have clearly brought out meso-level variations in hydrological categories. In addition, indirect energy balance estimates obtained from satellite images at different spatial scales can provide significant clues for better planning of water resources especially in design stage.