Estuarine bays serve as critical interfaces linking terrestrial and marine environments, yet the mechanisms governing the fate of hydrophobic organic contaminants (HOCs) within them remain inadequately constrained. Polycyclic aromatic hydrocarbons (PAHs) and organophosphate esters (OPEs), two extensively monitored priority pollutant classes, are ubiquitous in coastal systems; however, their coupled biogeochemical cycling in macrotidal, river-dominated estuaries is poorly understood. Here, we present a comprehensive summer survey (2025) of PAHs and OPEs across Hangzhou Bay to elucidate their distribution in seawater and sediments. Both contaminant classes were ubiquitously detected, exhibiting distinct compositional profiles between the aqueous and solid phases, reflecting differences in their physicochemical properties and phase-partitioning behaviors. Calculated adsorption–desorption coefficients (f_ad/de) revealed a pronounced net deposition trend for all target compounds, with PAHs demonstrating stronger sedimentary sequestration than OPEs due to their higher hydrophobicity and particle affinity. Notably, the slopes of linear regressions between sediment concentrations and total organic carbon (TOC) increased systematically with compound hydrophobicity (log KOW​), indicating that the sedimentary sequestration of PAHs and OPEs in Hangzhou Bay is primarily governed by organic-carbon-associated particle export mediated by the biological pump. These findings demonstrate that biologically mediated particle export overrides hydrodynamic mixing in controlling contaminant fate in productive estuaries, underscoring the necessity of integrating biological pump dynamics into coastal contaminant budgets and management frameworks.