Knowledge on the distribution of nitrogen (N) pools, processes, and fluxes along hydrological gradients provides a comprehensive perspective to understand the underlying causal mechanisms in intertidal flats, and thus improve predictions and climate adaptation strategies. We used a space-for-time substitution method to quantify N pools, processes, and fluxes along a hydrological gradient. Further, we linked N pools and processes and investigated not only surface but also subsurface sediments. Our results showed a gradual decrease in total N (TN) and mineralization rates (PN_min), but an increase in potential rates of nitrification (PNR) and denitrification (PDNR) under an elevated hydrological gradient, except for TN and PN_min in the subsurface sediment, which accumulated on the interaction zone between the high and middle tidal flats. Most sedimentary ammonium N (NH₄⁺) and nitrate N (NO₃⁻) concentrations were similar; however, NH₄⁺ accumulated on the subsurface of the middle tidal flat. NO₃⁻ fluxes (from −0.54 to −0.35 mmol m⁻² h⁻¹) were uptake fluxes in the intertidal flats, but NH₄⁺ fluxes (−2.48–3.54 mmol m⁻² h⁻¹) changed from uptake to efflux in the seaward direction. Structural equation modeling of the effects of inundation frequency, underground biomass, total carbon (TC), electrical conductivity (EC), and clay proportion on the N processes revealed that these accounted for 67%, 82%, and 17% of the variance of PDNR, PN_min, and PNR, respectively. Inundation frequency, underground biomass, TC, EC, and PN_min effects on N pools accounted for 53%, 69%, and 98% of the variance of NH₄⁺, NO₃⁻, and TN, respectively. This suggests that future sea level rise may decrease N storage due to increase in coupled nitrification–denitrification and decrease in N mineralization, and the NH₄⁺ flux may change from sink to source in intertidal ecosystems.