<p>Sea level rise and storm surges drive hydrologic disturbances that alter biogeochemical processes in upland forests, contributing to forest mortality and ecosystem state change. However, the impact of repeated flooding on belowground biogeochemistry in early stages of this transition is not well understood. We conducted a mesocosm flow-through incubation experiment, applying freshwater (FW) and brackish water (BW) pulses to intact soil monoliths (22&#xa0;cm depth × 22&#xa0;cm diameter) from a temperate upland coastal forest to understand how floodwater chemistry influences soil biogeochemistry and organo-mineral interactions. Continuous measurements of CO₂, CH₄, and N₂O fluxes were coupled with δ¹³C-CH₄ analysis, porewater chemistry (DOC, DIC,&#xa0;CDOM, SO₄²⁻, HS⁻, Fe²⁺, Mn²⁺, NH₄⁺, NO₃⁻ + NO₂⁻, Eh, pH), and Fourier-transform infrared spectroscopy (FTIR) of soil organic functional groups. BW treatments produced stronger legacy effects with enhanced reducing conditions, higher CH₄ and N₂O fluxes, and altered soil organic matter. Elevated HS⁻ concentrations and δ¹³C-CH₄ signatures indicated the co-occurrence of sulfate reduction and methanogenesis, likely via the methylotrophic pathway. Accumulation of NH₄⁺ and N₂O suggested dissimilatory nitrate reduction to ammonium, ammonium desorption via cation exchange, and incomplete denitrification. Increases in Fe²⁺, Mn²⁺, and DOC indicated carbon release via destabilization of organo-mineral associations, while FTIR revealed polysaccharide degradation and incorporation of sulfur- and nitrogen-containing groups. DOM optical indices showed smaller, more aromatic degradation products and a shift toward less humified, microbially derived organic matter from disrupted complexes. Our findings underscore the vulnerability of upland coastal forest soils to repeated inundation, with BW intrusion driving water chemistry-dependent feedbacks that destabilize soil carbon and may accelerate ecosystem transition.</p>