Based on the hydrological and meteorological data collected from 1919 to 1970 for Fenhe River Area, this study adopts the water-balance methods to estimate the water balance of the lakes in Taiyuan Basin in different periods of the last 2000 years in three aspects, i.e. lake surface waterfall, runoff into the lakes and lake surface evaporation. The study indicates that excluding the effect of runoff out of the lakes, the water capacity in the lakes of Taiyuan Basin remained surplus in all periods, which ensured the lakes’ existence; excluding the effect of runoff into the lakes, the water capacity was surplus only in the pre-Qin period. Therefore, runoff into the lakes is the decisive factor for the existence of the lakes in Taiyuan Basin. The extinction of lakes was directly affected by the rechanneling of Fenhe River. Year-on-year declines in runoff into the lakes led to continuous shriveling of the lakes. In contrast, runoff out of the lakes increased annually.