Based on the results of numerical calculations of the heat flow volume in the Northern Dvina River, two time periods of changes in the characteristic were identified. Changes in the thermal runoff over time proved to be heterogeneous, which is consistent with the results obtained for water temperature over the ice-free period. The two time periods in the heat flow regime of the Northern Dvina catchment were distinguished by changes in the near-surface air temperature, namely, a slight cooling from 1950 to 1975 and intense warming from 1976 to the present. The integral curve of average annual discharge through the Northern Dvina outlet gauging station at Ust-Pinega village was plotted for the period from 1950 to 2015, showing values exceeding the mean in the period starting 1976. An increase in the water temperature values over the ice-free period has been observed for all the observation sites since 1976. The average monthly volumes of heat flow during the ice-free period (May–October) were calculated for the two periods, showing that since 1976 the values were elevated at all sites in May and at most sites in July–October, whereas June heat flow was lower at all sites. The features of heat flow volume variation at the Ust-Pinega outlet are highlighted. The trend lines were declining in the first period and rising in the second period. Hence, the thermal regime of the Northern Dvina River flow changes more or less in line with the climate change, in particular its warming in the north.