The potential impact of natural factors on the runoff of intermittent rivers and ephemeral streams (IRES) has been largely ignored in the Tarim Basin, China. A representative example is the Keriya River. To quantify the long-term dynamic variations in lower reach surface runoff of IRES, river length, defined as the distance between a selected fix point along the perennial river segment to its dynamic, ephemeral end, was used as an indicator. Using a total of 272 remote sensing images, we digitized and measured the distance (river length) between the center of Yutian County and the river’s end point on each image, and then calculated monthly inter-annual and intra-annual variations in length of the lower Keriya River from 2000 to 2019. Hydrometeorological data were combined with descriptors of anthropogenic disturbances to assess the relative influence of natural factors and anthropogenic disturbances on lower reach river runoff. The results showed that intra-annual variations in river length fluctuated seasonally, with the minimum value occurring in June; two main peaks occurred in March and August. The minimum June value in river length was closely linked to an increase in agricultural water demand and a decrease in upper reach runoff. The August peak in river length was related to the peak values in upper reach runoff and agricultural water demand; upper reach runoff made a significant contribution because the former was about 20% more than the latter in summer. The March peak corresponded to elevated lower reach groundwater levels and to the melting of ice along river channels. Inter-annual variations in river length were due to inter-annual variations in upper reach runoff and middle reach agricultural water use which increased slightly during the study period. Inter-annual variations in frequency and amplitude of the fluctuations in river length were mainly controlled by changes in upper reach runoff. The minimum in river length in 2009 was consistent with the low in upper reach runoff of the Keriya River and other rivers in the Tarim Basin. The most significant factors controlling variations in river length are natural in origin.