Flow regulation mitigates drought-induced degradation of fish habitats in river-lake systems

• Assessment of fish community dynamics over the full hydrological cycle in China’s largest river–lake system. • Species-specific habitat suitability indices were applied to assess the drought-induced fish habitat degradation. • Flow regulation during early drought improved fish habitat, while delayed measures failed to reverse degradation. Extreme droughts are becoming increasingly frequent and severe worldwide, and river–lake systems respond in complex ways due to the intricate hydrodynamic coupling and competing interactions between fluvial and lacustrine components. Fish communities, as sensitive bioindicators, exhibit heterogeneous responses to these dynamics, further complicating drought-induced ecological impacts. Understanding these interconnected ecohydrological processes is crucial for developing effective ecological management strategies. This study investigated the full-cycle ecohydrological impacts of an unprecedented drought in the Yangtze River-Poyang Lake system, characterized by strong hydrological connectivity and high fish biodiversity. Fish community metrics and habitat suitability index (HSI) were used as diagnostic indicators. Multi-stage field surveys combined with hydrodynamic simulations and species-specific HSI assessments revealed that, drought onset led to highly constrained fish distributions and sharply declined fish connectivity within river–lake connecting channels, with the lacustrine side serving as a critical refuge and the fluvial side becoming a major bottleneck for river–lake fish connectivity. Despite initial habitat compression, the most severe degradation in HSI occurred post-drought, indicating ecological hysteresis. Species-level indicator responses varied: small-bodied opportunistic species showed rapid post-drought rebound, while large periodic strategists experienced prolonged declines, underscoring life-history-dependent vulnerability. Early-stage moderate flow regulation could jointly improve habitat suitability across all fish species by expanding the available hydraulic niche, whereas delayed interventions failed to reverse habitat degradation, highlighting the importance of threshold-based adaptive regulation (e.g., HSI < 0.4). These findings demonstrate the utility of HSI-based thresholds and fish community traits as ecological indicators to support adaptive, timely flow regulation strategies in response to intensifying droughts.