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Abstract The phases of long-lasting (more than 10–15 years) increased and decreased water flow, water temperature and heat flux values in the Northern Dvina River and the Pechora River were studied for the observation period from the 1930s to 2020. To distinguish between different phases, statistical homogeneity tests and normalized cumulative deviation curves were used. Generally, the identified phases displayed statistically significant differences between average values of the measured characteristics. During contrasting phases, the general pattern of water temperature during the warm season, water runoff and heat flux in the Northern Dvina and Pechora River Basins differed considerably. The number of the identified phases varied between the studied rivers and ranged from two to four contrasting phases in the Northern Dvina River exceeded those of the Pechora River. Consequently, the duration of the phases also varied quite significantly. The difference in mean values of the hydrological characteristics during the contrasting phases in the Northern Dvina River exceeded those of the Pechora River. The longest phases of increased and decreased heat flux nearly coincide with contrasting periods of water runoff and water temperature. The phases of simultaneous increased or decreased values of all hydrological characteristics were associated with corresponding periods of increased or decreased air temperature (on average for a year and for the open water period) and annual precipitation values. Those long-lasting phases of simultaneously increased or decreased values of river flow, heat flux, and water temperature were associated with changes of the global thermal regime, regional cryosphere variations, and long-term periods of intensification or weakening of the atmospheric circulation over the North Atlantic, characterised by variability in macrocirculation indices such as the North Atlantic Oscillation and Scandinavian circulation pattern.