Abstract: Seagrass beds serve as a globally important blue carbon ecosystem, and their carbon sequestration capacity and stability are highly sensitive to variations in hydrological and salinity conditions, especially under the intensifying pressures of global warming, sea-level rise, and anthropogenic disturbances. To clarify the response mechanisms of sediment carbon mineralization to changes in inundation depth and salinity, a 60-day laboratory incubation experiment was conducted using sediment samples collected from the seagrass beds in Caofeidian, Bohai Bay, China. We set three salinity levels (15‰, 25‰ and 35‰) and three inundation depths (0 cm, 1 cm, and 5 cm), forming a total of nine treatment groups with three replicates. Carbon mineralization rates and cumulative CO₂ emissions were dynamically monitored during the incubation period. Meanwhile, the dissolved oxygen and pH in the overlaying water, and total organic carbon, total nitrogen, total phosphorus and microbial community composition and diversity in sediments were analyzed to reveal the underlying regulatory pathways. The results showed that both increasing inundation depth and salinity significantly suppressed sediment carbon mineralization processes (p<0.05). Higher inundation depth and salinity levels consistently reduced both instantaneous carbon mineralization rates and total cumulative CO₂ emissions. Generalized linear model analysis indicated that inundation depth exhibited a significant negative effect on cumulative CO₂ emissions under all three salinity levels (p<0.01). Notably, the cumulative CO₂ emissions showed a significant temporal dependence only under the low-salinity condition (15‰), whereas no significant temporal dependence was detected under moderate (25‰) and high (35‰) salinity conditions, suggesting a strong modulation of salinity on the temporal dynamics of carbon mineralization. Two-way ANOVA analysis revealed a highly significant interactive effect between inundation depth and salinity on sediment carbon mineralization (F=7.58, p<0.01). The inhibitory effect of rising inundation depth on CO₂ emissions gradually was weakened with increasing salinity; similarly, the inhibitory effect of elevated salinity declined with increasing water table. These interactive patterns highlight the non-linear and compensatory nature of hydrological and salinity stressors in regulating coastal sediment carbon dynamics. Generally, both inundation depth and salinity shifts strongly reshaped the community structure and reduced the diversity of both bacteria and fungi. Under low inundation depth (0 cm) and low salinity (15‰), aerobic microbial groups with high metabolic efficiency, such as Talaromyces, Planococcus, Pseudomonas, and Bacillus, were dominant. In contrast, high inundation depth (5 cm) and high salinity (35‰) favored the growth of salt-tolerant, halophilic, facultative anaerobic, and low-efficiency microbial taxa, including Psychrobacter, Cobetia, Candida, Cystobasidium, sulfate-reducing bacteria, and methanogens. Correlation analysis further verified that carbon mineralization rates were significantly positively correlated with dissolved oxygen content and microbial diversity, but negatively correlated with inundation depth, salinity, and organic carbon content. Overall, inundation depth and salinity regulate sediment carbon mineralization through two coupled pathways, including altering environmental conditions (especially oxygen availability and pH) and filtering microbial functional groups to restructure community composition and metabolic pathways. The significant water–salt interaction alleviates the inhibitory effects under co-occurring high stress, which mediates the plasticity of carbon mineralization responses. These findings improve our mechanistic understanding of carbon cycling in coastal seagrass ecosystems under changing hydrological and saline environments, and provide essential data support and a theoretical basis for the effective conservation, restoration, and blue carbon management of seagrass bed ecosystems in the context of global environmental change.