Estuarine ecosystems are highly sensitive to climate change and anthropogenic forcing, often responding through regime shifts that emerge across multiple ecological dimensions. Here, using a unique phytoplankton dataset spanning more than 60 years (1960-2023), we provided strong evidence that the Yellow River Estuary (YRE) has experienced a tipping-point-mediated regime shift, manifested through coordinated changes in size structure and thermal traits. Over the past six decades, phytoplankton assemblages operated under a non-equilibrium regime, characterized by interannual turnover, episodic dominance amplification, and the absence of persistent species dominance. Since the early 2000s, however, phytoplankton communities transitioned toward a new structural state marked by miniaturization and thermophilization of dominant taxa. Most diatoms and warm- and temperate-affiliated species achieved dominance through reduced cell size, whereas dinoflagellates followed a contrasting pathway, attaining dominance primarily via episodic proliferation of large-bodied taxa. At the same time, the expansion of warm-water species reshaped community thermal composition and was associated with reduced compositional turnover, indicating a shift toward a more resistant and stabilized community state. Trait-based state-space analyses further demonstrated that downsizing and thermal changes were not gradual but instead reflected transitions between alternative states separated by distinct tipping boundaries. Tracking community trajectories relative to these boundaries showed that both thresholds were crossed during the 2000s, providing evidence for a regime shift in the YRE ecosystem. Mechanistically, warming, freshening, and nutrient imbalance acted interactively to trigger this regime shift through nonlinear, threshold-dependent responses. Overall, our findings illustrated how environmental forcing can reorganize estuarine ecosystems via trait reconfiguration and tipping-point dynamics, suggesting the significance of trait-based indicators and threshold awareness for assessing and managing ecosystem vulnerability under global change and human activities.

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