Studying water-level amplitude in plateau shallow lakes provides a critical perspective for understanding human–environment interactions and associated ecological risks. However, long-term continuous records of lake-level variation are scarce due to the relatively late establishment of modern monitoring. Using Qilu Lake in Yunnan Province as a case study, this research synthesizes multiple lines of evidence—including settlement distribution, palaeoshoreline geomorphology, historical documents, early maps, and remote sensing—to reconstruct seasonal lake extents (wet and dry seasons) for six representative years (1284, 1523, 1691, 1798, 1894, and 1937). Combined with documentary records, we further derive a characteristic series of water-level amplitude for the period 1284–1955. The results show that the main basin morphology remained generally stable under topographic constraints, while changes in lake extent were concentrated in reclamation-prone areas such as the shoals and deltaic margins along the western shore and the southern and northern shores. These changes are manifested as outward advancement of embankment lines and progressive enclosure of bays, with a gradual reduction in the space available for wet-season lake expansion. Over the past 600 years, the water-level amplitude of Qilu Lake exhibits a step-like decline superimposed on internal variability. Two notable downward shifts occurred around 1523 and 1691, marking phase changes in amplitude, whereas strong human intervention in outflow channels around 1894 did not trigger such a shift. Mechanism analysis indicates that variations in water-level amplitude were jointly driven by climatic windows and engineered interventions, with governance capacity acting as a key mediator. Specifically, warm–dry climatic phases provided implementation windows for reclamation, dredging, and outlet modification by lowering lake levels and promoting the stabilization of exposed lakebeds. Whether a downward shift in amplitude occurred depended on whether institutions could translate such short-term interventions into sustained engineering practices and maintain their effects over time. This study offers a traceable, process-based framework for identifying historical phase shifts and evaluating governance pathways in plateau shallow lakes.