Hysteresis in floodplain lakes occurs between stage and lake area. Stage-area hysteresis controls the storage and exchange of water and sediments, and is a critical hydrological behavior for lake management. While hysteresis has been repeatedly observed in the floodplain lakes of large rivers, the hydrological mechanism and factors in control have been poorly understood thus far. In this paper, we investigate the role of geomorphology in controlling lake hysteresis, specifically the geologic setting and the lake basin, the lake position relative to the main stem of the river, as well as the influence of lake shape and its internal depositional landforms on inundation dynamics. We study the floodplain lakes along three of the largest rivers around the world: the Curuai Lake of the Amazon River, the Tonle Sap Lake of the Mekong River, and the Poyang Lake of the Yangtze River. The three lakes exhibit a similar counter-clockwise stage-area hysteresis: for a given stage, the lake area is larger in the falling season than in the rising season. Our results indicate that hysteresis is mainly controlled by geomorphology, where the lake shape and basin size lead to delays in the drainage and drop in lake area during the falling season, resulting in counter-clockwise hysteresis. Nevertheless, the lakes are of distinct climatic and geologic-geomorphic settings, representing the variety in the lake types of large rivers. Hence, while geomorphology is the overall driver, unique lake characteristics delay the fall in water extent and shape hysteresis on a case-by-case nature. At Curuai, the complex floodplain morphology (impeded floodplain) complicates and slows the routing of outflow. At Tonle Sap, the lake flows into the river solely through a narrow channel, where a backwater effect restricts drainage. At Poyang, the wide lake shape upstream leads to counter-clockwise hysteresis, while the narrow channel downstream exhibits clockwise hysteresis. Out of the three investigated floodplains, Tonle Sap has the largest degree of hysteresis (0.41), followed by Poyang (0.17) and Curuai (0.13). This trend in hysteresis extent is a result of the different composition of inflow and the lake–river hydrological connectivity, attributed to lake geomorphology. This study is the first to address geomorphology as the primary control over lake hysteresis, which improves understanding of the stage-area curve in empirical and numerical hydrological models, and potentially floodplain management.