Satellite‐geodetic altimetry investigations in the Karakoram have indicated slight mass gain or loss of the glaciers during the early part of 21st century. Equivalent discharge in the upper Indus Basin due to these mass changes has been estimated at 5 to 10% of mean annual flow. However, satellite altimetry and geodetic glacier mass estimates in the extreme topography of the Karakoram have not yet been counter‐validated by hydrological analysis. Therefore, we present a first cross validation of three to five decades of river flow data from the three major watersheds in the Karakoram, with matching series of monthly precipitation, temperature, and evaporation provided by six atmospheric reanalysis products for 1979–2014. The analyses suggest that in most cases river flows have been increasing steadily from the end of the 1960s and 1970s to the middle of the 1990s and have stabilized or are in decline since then. Hunza watershed in Karakoram West shows consistently declining flows over the first half of the analysis period and stable flows during the second half for most of the summer melting season, suggesting mass accumulation. Rising river flows in the Shyok and Shigar watersheds, followed by stabilizing or slightly declining flows from 1995 onward, can be explained by consistently increasing precipitation during the first half of the analysis period, and successive stabilization or minor decline thereof. Flow data do not necessarily suggest considerable loss or gain of glacial mass in the Karakoram during the late 90s and early 2000s as suggested by satellite‐based altimetry studies.