Estuary–bay systems are critical land-to-sea interfaces for microplastics (MPs). While marine sediments are considered the ultimate MP sink, hydrodynamic controls on retention and burial remain poorly quantified. This study integrates field observations, numerical modeling, and aging fingerprint analyses to investigate MP source-to-sink dynamics across multiple estuary–bay systems in China’s Zhejiang coastal region, including the Qiantang River Estuary, Xiangshan Bay, Hangzhou, Sanmen, Wenzhou Bays, and the Zhoushan Archipelago. We first quantified riverine MP inputs. In the Qiantang River, tributaries amplify MP load by >20-fold, delivering ~2,831 tons/year to Hangzhou Bay. In Xiangshan Bay, particle tracking shows only ~17% of MPs are exported offshore; most undergo tidal oscillations, making the bay a “temporary reservoir” rather than a permanent sink. Mass-balance modeling across three bays confirms transient storage, with riverine contributions of 41.5–96.7% and retention times of days to weeks. To explain the decoupling between settling flux and sedimentary abundance, we developed a coupled hydrodynamic–particle tracking model resolving settling–resuspension cycles. We introduced three key metrics—settling flux (F_s), resuspension period (T_resus), and mean residence time (τ_resi)—to quantify bed shear stress controls. Counterintuitively, F_s correlates negatively with seabed MP abundance, challenging the “high-input, high-deposition” paradigm. Instead, τ_resi emerges as the master variable controlling burial efficiency. τ_resi is governed by the hydrodynamic “temporal structure”: the exceedance time proportion (R) promotes deposition via sustained low-stress windows, while exceedance frequency (f) destabilizes the bed through frequent disturbances. This dual control exhibits nonlinear threshold effects, with f weakening R’s dominance above ~60–110 exceedance events per month. We also explored MP aging fingerprints—carbonyl index (CI) and fouling index (FI)—as independent tracers of transport history. In the Zhoushan Archipelago, CI correlates positively with transport time, with FI showing stronger correlation, suggesting aging indicators can constrain model-derived τ_resi. Anomalously high aging in high-disturbance zones reveals a “resuspension-amplified aging” effect, where repeated burial–exposure cycles accelerate degradation beyond apparent transport time. Collectively, this work proposes a “dynamic sink” framework that redefines the marine MP sink from a static repository to a temporally explicit screening process governed by quantifiable hydrodynamic thresholds, providing a mechanistic basis for predicting accumulation hotspots, identifying stable burial versus active release zones, and informing targeted management strategies. This framework is transferable to other estuary–bay systems worldwide.