A direct connection between the peculiarities of watershed land cover and the structure of annual river flow isestablished. The research is based on approaches elaborated by the author using GIS-technologies. It has been done on example of two watersheds located in upper reaches of the Andoma and Ema river basins, Vologda region. It is shown that replacement of forest areas by farmlands results in increase of intra-annual river flows fluctuations. Spring floods and low water summer and winter seasons are intensified.