A 606 year runoff reconstruction of the Kara Darya River was developed, based on the tree-ring width chronology of Turkestan juniper (Juniperus turkestanica) from the Pamir-Alai Mountains of Kyrgyzstan. Preliminary comparison between the snow cover variation and these climate/runoff reconstructions found that Central Asian snow cover may have strong associations with large-scale ocean-atmosphere-land circulations. The runoff reconstruction demonstrated that instrumental runoff was not representative of runoff over the past 606 years. The drought of the 1960s-1990s resulted in low runoff levels during the past 50 years; however, this probably does not represent a worst-case scenario for the Kara Darya because the runoff reconstruction showed additional extremely low runoff prior to the 20th century. The reconstruction will provide a long-term perspective on runoff variation in the Kara Darya River basin, aid sustainable water resource management and be useful in guiding expectations of future variations and water resource planning.