A comprehensive multi-component reactive transport model is being developed to explain hydrochemical observations in a subterranean estuary (STE) below a real high-energy beach. The aim of the modelling is to explore and quantify the individual boundary condition effects on the hydrochemical processes and related water quality changes within the STE. It is still work in progress. The reactive transport model is based on an existing conservative flow and transport model calibrated against measured hydraulic heads, seasonal temperatures, and apparent Tritium/Helium groundwater ages. The reactive transport model considers the degradation of organic matter and the corresponding terminal electron acceptor processes (TEAPs) aerobic respiration, nitrate reduction, as well as sulfate and iron reduction. Calcite, siderite and FeS precipitation/dissolution were also included. The model further considers temperature dependent reaction kinetics of the TEAPs. The observed distribution of dissolved ferrous iron, alkalinity, pH, and ammonium could be well replicated, while the simulated patterns and dynamics of dissolved oxygen and nitrate were less accurate. The observed and simulated iron concentrations in the tide-induced upper saline plume (USP) and its fringes were up to 25 µmol/L. In the freshwater dominated zones of the STE, lower simulated iron concentrations of ~1 µmol/L were found, in line with field observations from the freshwater lens. The increased iron concentrations within the seawater affected zones of the STE was caused by the increased solubility of iron-bearing minerals as a result of elevated ionic strength. Within the USP, iron-oxide precipitation occurred at the thin redox boundary from nitrate- and iron reduction due to hydrodynamic dispersion. The location of this redox boundary shifted with time in response to the seawater infiltration dynamics depending on oceanic forcing.