The operation of large-scale reservoirs have modified water and sediment transport processes, resulting in adjustments to the river topography and water levels. The polynomial fitting method was applied to analyze the variation characteristics of water levels under different water discharge values in the Jingjiang reach of the Yangtze River from 1991-2016. The segregation variable method was used to estimate the contributions of the varied riverbed evaluation, the downstream-controlled water level, and the comprehensive roughness on the altered water level at an identical flow. We find that low water levels in the Jingjiang reach of the Yangtze River from 1991-2016 are characterized by a significant downward trend, which has intensified since 2009. Riverbed scouring has been the dominate factor causing the reduced low water level while increased roughness alleviated this reduction. From 1991-2016, there was first a decrease followed by an increase in the high water level. The variation characteristic in terms of the “high flood discharge at a high water level” before 2003 transformed into a “middle flood discharge at a high water level” since 2009. The increased comprehensive roughness was the main reason for the increased high water level, where river scouring alleviated this rise. For navigation conditions and flood control, intensified riverbed scouring of the sandy reaches downstream from dams enhanced the effects that the downstream water level has on the upstream water level. This has led to an insufficient water depth in the reaches below the dams, which should receive immediate attention. The altered variation characteristics of the high water level have also increased the flood pressure in the middle reaches of the Yangtze River.