A 2,500-year sedimentary record reveals cryptic ecological degradation in a macrophyte-dominated Yangtze floodplain lake

Lake Liangzi, a shallow floodplain lake in the middle reaches of the Yangtze River, is listed in the Asian Wetland Protection Directory for its critical ecosystem services. However, the loss of ecological resilience in macrophyte-dominated lakes subjected to long-term eutrophication pressure is often underestimated when dense vegetation cover persists. Using a continuous 2,500-year sedimentary sequence, we reconstruct the long-term ecological evolution of Lake Liangzi through the integration of sedimentary ancient DNA (sedaDNA), plant functional traits (life form and canopy height), and multi-proxy geochemical indicators. The sediment record reveals three distinct ecosystem phases. During an early stable state (2610–1550 cal yr BP), oligotrophic conditions supported diverse submerged and floating-leaved macrophyte communities within a modular ecological network. This was followed by an adaptive transition phase (1550–344 cal yr BP), during which early anthropogenic disturbance increased nutrient inputs and promoted opportunistic taxa, while overall community evenness and resilience were maintained. In the most recent phase (344 cal yr BP–present), intensified catchment erosion and eutrophication progressively degraded underwater light conditions. Rather than collapsing, the ecosystem persisted through trait-mediated adjustment: the canopy-forming species Potamogeton maackianus achieved monodominance by increasing community-weighted plant height, competitively excluding floating-leaved and benthic taxa. Sedimentary network reconstructions indicate that this persistence masked a fundamental structural shift from a diverse, modular system to a highly connected and fragile regime. Our results demonstrate how long-term sedimentary archives can reveal “cryptic degradation” processes that are not evident from present-day vegetation cover alone. This study highlights the value of multi-proxy lake sediment records for quantifying long-term ecosystem trajectories, resilience loss, and the delayed risks of regime shifts in human-impacted freshwater systems.