Abstract The Kara Sea, due to its geographic location downstream of the main eastward Atlantic Water inflow through the Barents Sea, is strongly influenced by the history of the Atlantic Water masses which enter at its western entrances: the Kara strait and the passage between Franz Josef Land and Novaya Semlya. Little is known about the interannual variability of temperature, salinity and volume fluxes through these entrances. The present investigation analyzes model results from 1979 to 1999 and compares them to hydrographic observations in the Barents and Kara seas with respect to the interannual variability of Atlantic Water flow through the western entrances of the Kara Sea. Model results and observations suggest the propagation of sequences of warm and cold anomalies through the area of investigation. Most prominent are anomalously cold years 1986, 1993 and 1998 for the Kara Strait throughflow which are associated with weak eastward or even westward flow over periods up to several months. For the passage between Franz Josef Land and Novaya Semlya, the entire period of the 1990s is characterized by warm deep water temperatures. In the early and late 1990s also the eastward volume fluxes are at their maximum. We discuss an Empirical Orthogonal Function analysis of the velocity in the Barents and Kara Seas. The warm and cold phases are associated with the first two modes of the velocity pattern in the domain. The links of these velocity patterns with the large scale sea level pressure are discussed.