River–lake systems in the middle and lower reaches of the Yangtze River Basin function as critical ecological interfaces for maintaining regional water security and biodiversity. However, the complex interplay between environmental factors and biological communities in these systems remains poorly understood, limiting evidence-based management strategies essential for achieving sustainable development goals. This study investigated the spatiotemporal heterogeneity of environmental variables and their relationships with biological communities across 36 sampling sites (4 rivers, 5 lakes) from January to November 2022. Significant spatial differences were observed between river and lake systems, with lakes exhibiting higher concentrations of biochemical oxygen demand (BOD₅), chlorophyll-a, permanganate index (CODMn), loss on ignition (LOI), sediment total nitrogen (STN), total organic carbon (TOC), and turbidity, while rivers showed elevated total nitrogen levels. These patterns reflected fundamental differences in hydrodynamic mechanisms, particularly water retention time and sedimentation processes. Environmental parameters displayed distinct seasonal variations, with BOD₅ increasing markedly in autumn, and chlorophyll-a showing system-specific peaks in lakes (May) and rivers (September). Multivariate analyses revealed that water temperature, organic matter, and nutrients (particularly phosphorus) were key drivers shaping both phytoplankton and benthic communities. The structural equation model identified a strong cascade pathway from turbidity through phosphorus to phytoplankton richness, and uncovered a “phosphorus paradox” wherein total phosphorus exhibited contrasting effects on different biological components—positive for phytoplankton richness but negative for benthic richness. The positive relationship between phytoplankton and benthic macroinvertebrate richness provided evidence for benthic–pelagic coupling in this river–lake system. These findings advance our understanding of the complex mechanisms linking physical factors, nutrient dynamics, and biological communities across river–lake continuums, providing a quantitative framework for ecosystem-based management that supports sustainable development in the Yangtze River Basin and similar freshwater systems globally.

Reconciling hydropower development with aquatic biodiversity conservation is a central challenge for sustainable river management worldwide. Cascade dam configurations, in which multiple impoundments are arranged in series along a single channel, impose longitudinal environmental gradients that restructure biological communities across trophic levels. Whether the resulting multi-trophic responses are independently driven by shared abiotic gradients (environmental filtering) or mechanistically coupled through direct food-web interactions (trophic cascading) remains unresolved. We surveyed phytoplankton, zooplankton, and benthic macroinvertebrates simultaneously at seven stations along a 430 km gradient downstream of Danjiangkou Dam in the Hanjiang River, the largest tributary of the Yangtze River and the source of China’s South-to-North Water Diversion Middle Route, over eight seasonal campaigns (2015–2017). Variance partitioning, piecewise structural equation modeling, Mantel tests, and co-occurrence network analysis were applied to partition environmental and trophic pathways. Environmental filtering dominated community restructuring at all three trophic levels, while the biotic proxy for direct trophic interactions explained less than 0.4% of community variation, consistent with weak detectable trophic coupling at seasonal resolution. Distance from Danjiangkou Dam shaped downstream transparency and turbidity gradients that mediated trophic-level-specific responses along distinct environmental axes (pH and water temperature for phytoplankton, conductivity for zooplankton, and transparency for benthic macroinvertebrates). Benthic macroinvertebrates were systematically decoupled from the pelagic analytical framework, absent from the cross-trophic co-occurrence network and structured more by spatial configuration than by water-column variables. Hub species in the network were associated with downstream mineralized conditions, confirming that network architecture reflects shared environmental preferences rather than biotic interactions. These findings support a management shift from single-dam mitigation toward cascade-scale coordination of environmental flow regimes, sediment connectivity, and substrate restoration as integrated strategies for sustaining multi-trophic biodiversity in regulated rivers.

Shallow eutrophic lakes recover from nutrient loading on time scales ranging from less than one year to many decades, yet whether this range is set by the lake or by the biological response group has rarely been quantified within a single monitoring framework. We assembled a five-year (2020–2025) quarterly monitoring panel from three shallow Yangtze-floodplain lakes (Lake Changhu, Lake Liangzihu, and Lake Honghu; 15 stations, 21 quarters) and applied a panel mixed-effect distributed lag model (PME-DLM) to estimate the lag-response windows of phytoplankton and benthic macroinvertebrate densities against five water-quality drivers. Cross-lake consistency was tested with a station-resampled bootstrap, and the contributions of water quality, season, and lake identity to community variation were resolved by three-table variation partitioning. The PME-DLM resolved a 3-month temperature window for phytoplankton and 9–15 month chlorophyll a and temperature windows for benthic communities, while total nitrogen and total phosphorus were non-significant in either group. Cross-lake bootstrap intervals on window width overlapped substantially across the three lakes, whereas cross-group differences in window centre and shape were an order of magnitude greater. Variation partitioning further showed a mirror-image structure in which phytoplankton variation was dominated by the pure water-quality fraction (12.2%) and benthic variation by the water-quality × season joint fraction (5.8%). Within the resolution of this five-year, three-lake panel, group-level differences in lag-response time scale were more apparent than lake-level differences and provide a quantitative basis for matching restoration assessment cadence to pelagic versus benthic recovery.