The global renewable energy potential estimates vary hundredfold, while the estimates for global hydropower vary fourfold. Thus, an accurate method of assessing the small hydropower (SHP) potential at regional and (sub)-national scales is required. This study aims to present and verify a robust method for sizing and siting the SHP potential by utilizing the capabilities of GIS. The proposed virtual hydropower assessment (VHA) method identifies suitable locations for hydropower production based on digital elevation and specific discharge maps. VHA was conducted for Estonia, a low-lying country in Europe. Twenty operational or abandoned SHP in thirteen rivers were used for verification. There is a good overall agreement between the computed virtual and installed capacities. The VHA method provided a realistic output for SHP location siting and revealed some unexploited opportunities to install micro and mini-hydro schemes in all of the analyzed rivers. Further research is required with a larger verification data sample for the VHA method to investigate the effects of the digital elevation model resolution, river segment length, and hydrological components. The outcomes of this study provide a reliable and robust method of assessing the SHP potential worldwide, particularly in countries where meteorological and hydrological data are scarce.