Subtropical coastal bays significantly mediate land-ocean carbon fluxes, yet their responses to concurrent warming and intensified river discharge remain unclear. Using monthly observations over a decade in Xiamen Bay and integrating flow cytometry, high-throughput sequencing, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and NanoSIMS carbon tracing, we explored how microbially driven carbon cycling responds to these dual forces. Our findings reveal that under present-day conditions, a +4 °C warming would increase the abundances of Synechococcus (∼19%) and microeukaryotic algae (∼5%), suggesting an enhanced potential for labile dissolved organic matter (LDOM) production. NanoSIMS experiments showed a 5-fold increase in heterotrophic bacterial assimilation of phytoplankton-derived carbon at elevated temperatures (30 °C versus 22 °C). Concurrently, intensified riverine discharge delivered terrestrial recalcitrant DOM (RDOM), altering DOM molecular composition and decreasing overall bioavailability. These combined stressors restructured microbial communities, accelerating heterotrophic carbon processing and reducing the ratio of ecologically persistent DOM to recalcitrant dissolved black carbon. We propose a Dual-DOM Forcing framework that formalizes how thermal (autochthonous LDOM) and hydrological (allochthonous RDOM) drivers jointly regulate microbial carbon processing, DOM persistence, and coastal carbon sequestration potential. This framework provides a transferable basis for assessing the vulnerability of coastal blue carbon sinks to concurrent warming and altered river discharge.