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Coastal aquifers experience water table fluctuations that push and pull water and air through organic‐rich soils. This exchange affects the supply of oxygen, dissolved organic carbon (DOC), and nitrogen (N) to shallow aquifers and influences groundwater quality. To investigate the fate of N species, we used a meter‐long column containing a sequence of natural organic topsoil and aquifer sediments. A fluctuating head was imposed at the column bottom with local, nitrate‐rich groundwater (16.5 mg/L NO₃‐N). We monitored in‐situ redox potential and collected pore water samples for analysis of inorganic N species and DOC over 16 days. Reactive processes were more complex than anticipated. The organic‐rich topsoil remained anaerobic, while mineral sediments beneath alternated between aerobic, when the water table dropped and sucked air across preferential flow paths, and anaerobic conditions, when the water table was high. A fluid flow and reactive transport model shows that when the water table rises into organic‐rich soils, it limits the flow of oxygen, while the soils release DOC, which stimulates the removal of nitrate from groundwater by denitrification. At the end of the experiment, we introduced seawater to the column to mimic a storm surge. Seawater mobilized N and DOC from shallow soil horizons, which could reach the aquifer if the surge is long enough. These processes are relevant for groundwater quality in developed coastal areas with anthropogenic N sources, as climate change and rising seas will drive changes in water table and flood dynamics.