Multi-Level Driving Mechanisms: Cascading Relationships Among Physical Factors, Nutrient Cycling, and Biological Responses in the Yangtze River–Lake Ecosystems

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.