River discharges from Siberia are a large source of freshwater into the Arctic Ocean, whereas the cause of the long-term variation in Siberian discharges is still unclear. The observed river discharges of the Lena in the east and the Ob in the west indicated different relationships in each of the epochs during the past 7 decades. The correlations between the two river discharges were negative during the 1980s to mid-1990s, positive during the mid-1950s to 1960s, and became weak after the mid-1990s. More long-term records of tree-ring-reconstructed discharges have also shown differences in the correlations in each of the epochs. It is noteworthy that the correlations obtained from the reconstructions tend to be negative during the past 2 centuries. Such tendency has also been obtained from precipitations in observations, and in simulations with an atmospheric general circulation model (AGCM) and fully coupled atmosphere–ocean GCMs conducted for the Fourth Assessment Report of the IPCC. The AGCM control simulation further demonstrated that an east–west seesaw pattern of summertime large-scale atmospheric circulation frequently emerges over Siberia as an atmospheric internal variability. This results in an opposite anomaly of precipitation over the Lena and Ob and the negative correlation. Consequently, the summertime atmospheric internal variability in the east–west seesaw pattern over Siberia is a key factor influencing the long-term variation in precipitation and river discharge, i.e., the water cycle in this region.