Within the river-estuary-bay continuum, intertidal wetlands act as a critical biogeochemical filter, where sedimentary nitrate reduction pathways determine whether nitrogen is permanently removed via denitrification or retained as ammonium through dissimilatory nitrate reduction (DNRA). The balance between removal and retention has profound implications for downstream water quality. However, how hydrological perturbations, particularly altered inundation regimes, tip this balance remains poorly understood. Using an 18-month manipulative experiment across a gradient of inundation frequency, combined with isotope tracing and metagenomics, we identified a distinct hydrological threshold that governs the partitioning of nitrate reduction pathways in both mangrove and unvegetated sediments. Below this threshold, oxidized conditions favour denitrification and effective nitrogen removal. Once inundation exceeds the threshold, the system shifts towards DNRA dominance, converting nitrate to ammonium rather than removing it. Notably, this transition is amplified in vegetated sediments, revealing a tight coupling between plant survival and below-ground microbial function. These findings challenge the conventional view of intertidal wetlands as simple nitrate sinks. They instead reveal a nonlinear response, where the removal versus retention balance depends critically on inundation regimes. As sea-level rise and upstream flow regulation continue to reshape tidal hydrology along the land-sea continuum, our threshold-based framework provides a basis for assessing when and where these ecosystems might transition from water quality regulators to internal nitrogen sources, with direct implications for coastal management and restoration.