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The mixing of terrestrial groundwater and seawater creates dynamic reaction zones in intertidal areas, where land-derived Fe(II) is oxidized to Fe(III) and then precipitates as Fe hydroxides at the groundwater–seawater interface. These hydrogeochemical processes contribute to the formation of iron bands at the saltwater wedge (SW) and beneath the upper saline plume (USP). This study provides a comprehensive review of physical and geochemical processes at field scale in coastal areas, explores the impact of mineral precipitation on pore structure at pore scale, and synthesizes reactive transport modeling (RTM) approaches for illustrating continuum-scale soil physio-chemical parameters during the evolution of porous media. Upon this review, knowledge gaps and research needs are identified. Additionally, challenges and opportunities are presented. Therefore, we reach the conclusion that the incorporation of observational data into a comprehensive physico-mathematical model becomes imperative for capturing the pore-scale processes in porous media and their influence on groundwater flow and solute transport at large scales. Additionally, a synergistic approach, integrating pore-scale modeling and non-invasive imaging, is equally essential for providing detailed insights into intricate fluid–pore–solid interactions for future studies, as well as facilitating the development of regional engineering-scale models and physio-chemical coupled models with diverse applications in marine science and engineering.