Water level and streamflow extracted from 891 hydrological episodes from both dry and flood seasons covering a period of 1954–2009 were analyzed to investigate stage–flow relations. Results indicate the following. (1) Since the early 1990s the low/high flow is increasing/decreasing. The water level, particularly the high level, is consistently decreasing. An abrupt decrease of water level is observed since the early 1990s at the lower East River. (2) Stage–streamflow relation is usually stable in the river reach with no significant bedform morphological changes. Changes in the geometric shape of the river channel are the major cause of the change in the stage–streamflow relation. (3) An abrupt decrease of water level at the Boluo station is mainly the result of abnormally rapid downcutting of the riverbed due to extensive sand dredging within the channel which caused serious headwater erosion. This human-induced modification by downcutting of the river channel may lead to significant hydrological alterations and may have critical implications for flood control, conservation of eco-environment, and also for basin-wide water resources management in the lower East River basin.