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Abstract. Prediction of mean annual runoff is of great interest but still poses achallenge in ungauged basins. The present work diagnoses the prediction inmean annual runoff affected by the uncertainty in estimated distribution ofsoil water storage capacity. Based on a distribution function, a waterbalance model for estimating mean annual runoff is developed, in which theeffects of climate variability and the distribution of soil water storagecapacity are explicitly represented. As such, the two parameters in themodel have explicit physical meanings, and relationships between theparameters and controlling factors on mean annual runoff are established.The estimated parameters from the existing data of watershed characteristicsare applied to 35 watersheds. The results showed that the model couldcapture 88.2 % of the actual mean annual runoff on average across thestudy watersheds, indicating that the proposed new water balance model ispromising for estimating mean annual runoff in ungauged watersheds. Theunderestimation of mean annual runoff is mainly caused by theunderestimation of the area percentage of low soil water storage capacitydue to neglecting the effect of land surface and bedrock topography. Higherspatial variability of soil water storage capacity estimated through theheight above the nearest drainage (HAND) and topographic wetness index (TWI)indicated that topography plays a crucial role in determining the actualsoil water storage capacity. The performance of mean annual runoffprediction in ungauged basins can be improved by employing better estimationof soil water storage capacity including the effects of soil, topography,and bedrock. It leads to better diagnosis of the data requirement forpredicting mean annual runoff in ungauged basins based on a newly developedprocess-based model finally.