Salinization is a worldwide issue particularly threatening arid and semi-arid soils. Primary salinization is due to unbalanced flows between upward water and solute flows leading to salts accumulation and downward flows which allow the leaching of salts. Soil salinity affects vegetation by causing osmotic and toxic stress. In return, soil water transfers are impacted since water extraction by plants is limited. Salinity leads also to a decrease of soil hydraulic conductivity. Salinisation is often described as a threat to agriculture, but less as a driver of specific ecosystem functioning, such as salt marshes. These interfaces between land and sea are very present in the Mediterranean deltas and lagoon complexes, and provide several ecosystem services, (e.g. being the natural areas among with the highest carbon storage rate). Salinity in these ecosystems is highly dependent on freshwater inputs from precipitation, natural or anthropic flooding, making them vulnerable to global changes. Nevertheless, the effects of flooding on hydrological dynamics and solute transfers in salt marshes are not well known. We choose a study site in the lowlands of the Aude river (the Castelou site, Narbonne, France) to address the question of the hydrological behavior of a salt marsh managed by different flooding intensities in relation to plant communities. Soil moisture, saturated zone depth, and salinity dynamics are monitored by a set of continuous and point measurements at 12 sites distributed along a flood management gradient and a natural salt pressure gradient. Based on these observations, time continuous data series have been built by a physics-based modeling. The analysis provides a better understanding of the effects of flooding on soil water and solute stocks and fluxes, and relates them to the specific composition of plant communities. We show that flooding has varying effects on water storage in unsaturated and saturated zones. Soil water recharge has a small effect on s