In the rivers of the central part of the East European Plain (the Volga at Staritsa, the Oka at Kaluga, and the Don at Stanitsa Kazanskaya), long phases (10–15 years or more) of increased/decreased annual and seasonal runoff have occurred, as well as differences in the frequencies of extremely low flow conditions from the late 19th century to 2020. Phase boundaries were identified by cumulative deviation curves and statistical homogeneity. The frequencies of specific water flow values were estimated using the empirical curves of the exceedance probability of annual and seasonal water flows based on their long-term time series. In the century-long changes of rivers considered, two long contrasting phases were revealed. These phases are characterized by increased and decreased runoff of hydrological seasons. Near simultaneously, a phase of increased runoff was first observed for the freshet season. On the contrary, phases of decreased runoff were first observed for low-water seasons. The runoff phases differ significantly in duration and differences in flow. Significant differences were revealed in the frequency of low-water years for a low runoff with an exceedance probability above or equal to 75% and above or equal to 95%.