The aim of this study was to assess the climatic changes in the annual river runoff of the Northern Okhotsk Sea region within the Magadan region. In the present work the analyzed series end with data for 2019. Observation series of river runoff at eight hydrological stations were used in this work. By the method of hydrological analogy, these series were brought to a multiyear period by restoring year-on-year values. Thus, the series of annual runoff for 1958–2019 were analyzed. The research method was the analysis of runoff time series for the presence of homogeneity in the mean (Student’s criterion), as well as spectral analysis. Comparison of mean long-term values of runoff layers for two periods (1958–2000 and 2001–2019) showed that the “norm” increased by 5–37%. It should be noted that these changes are not random according to the Student’s criterion with significance level of 5%. The presence of a trend in long-term water availability fluctuations is also evidenced by the time course of the dynamic mean annual runoff. Analysis of the runoff series, mean annual air temperature and total annual precipitation made it possible to conclude that annual runoff increase is caused by climatic changes, mainly by an increase in precipitation. It is possible that runoff increase is also due to the thawing of ice in the permafrost strata. But you should pay attention to the fact that with climate warming, moisture losses for evapotranspiration increase, primarily due to the growth of trees and shrubs. Moreover, this effect is more noticeable in large catchments. A 6-year cyclicity was revealed in the long-term fluctuations of annual runoff. These fluctuations are most likely a non-stationary complex Markov process. The results of this work will be useful for hydrological calculations, long-term and ultra-long-term runoff forecasts, and studying the river – sea ecosystems. Further hydrological studies should be carried out with the obligatory study of evapotranspiration in various landscape conditions.