Significantly increased sedimentation rates (SRs) in lakes worldwide in recent decades due to higher inputs of silt and eutrophication have led to significant environmental problems such as lake size diminishment and degraded water quality. Many lakes in the middle and lower reaches of the Yangtze River basin (MLYB) have followed this pattern. For effective lake management, it is essential to understand the pattern and drivers of SRs in these lakes. Fourteen typical lakes in the MLYB were chosen to examine the spatiotemporal patterns of SRs and identify the drivers over different time periods. Since 1900, SRs increased from <0.2 to 0.3–0.6 g·cm⁻²·year⁻¹, particularly notable during 1930–1990. Combined with climatic factors, SR correlated negatively with lake (catchment) size and abundance of aquatic vegetation, whereas other lake features including nutrient status did not contribute significantly to the variation in SRs, due to the fast decomposition processes of organic matter in shallow lakes. Detrimental land use practices especially reclamation for croplands and rapid urbanization was revealed to elevate SRs pronouncedly. We propose various management strategies aiming to maintain SR reference condition at ~0.16 ± 0.08 g·cm⁻²·year⁻¹, which is analogous to the SR value between 1850 and 1900.