Disagreements across different reanalyses over South Asia result into uncertainty in assessment of water availability, which is computed as the difference between Precipitation and Evapotranspiration (P-E). Here, we compute P-E directly from atmospheric budget with divergence of moisture flux for different reanalyses and find improved correlation with observed values of P-E, acquired from station and satellite data. We also find reduced closure terms for water cycle computed with atmospheric budget, analysed over South Asian landmass, when compared to that obtained with individual values of P and E. The P-E value derived with atmospheric budget is more consistent with energy budget, when we use top-of-atmosphere radiation for the same. For analysing water cycle, we use runoff from Global Land Data Assimilation System, and water storage from Gravity Recovery and Climate Experiment. We find improvements in agreements across different reanalyses, in terms of inter-annual cross correlation when atmospheric budget is used to estimate P-E and hence, emphasize to use the same for estimations of water availability in South Asia to reduce uncertainty. Our results on water availability with reduced uncertainty over highly populated monsoon driven South Asia will be useful for water management and agricultural decision making.