The installation of desalination plants close to ecosystems of interest may have environmental impacts that make corrective measures necessary. Especially, wetlands (which are water-dependent ecosystems) are prone to degradation. This is the case for the Agua Amarga salt marsh (SE Spain), that includes an abandoned solar saltworks and surrounding, topographically higher zones, in which the groundwater withdrawal to supply two desalination plants has led to a drop of the piezometric levels and the desiccation of the ecosystem. To overcome these problems, a programme to irrigate the marsh with seawater was established. This paper reports some soil characteristics of the marsh in relation to the different types of vegetation/environment identified and the seawater irrigation programme, with the objective being to propose some guidelines to improve the management of the site. Surface and subsurface samples were taken from 63 plots and the depth of the water level and the soil redox potential (Eh), moisture, electrical conductivity (EC), CaCO3, organic carbon, nitrogen and bulk density were determined. Also, the soil texture, structure, consistence, accumulation of salt crystals and redoximorphic features – indicative of reduction-oxidation processes – were described. The poor structure (weak, granular, subangular and angular blocks, very fine and fine) showed that the soils were hardly developed. The periphery (mainly colonised by Suaeda vera, Lygeum spartum and Limonium spp.) was less saline (EC 1:5 in the upper layers ~0.4 to ~4dSm−1) and drier (water level>−1.5m depth) than the abandoned saline ponds (EC 1:5 in the upper layers ~2 to ~9dSm−1 and water level between −1m depth and +0.2m above the soil surface), mainly colonised by Sarcocornia fruticosa, Arthrocnemum macrostachyum, Salicornia patula, Phragmites australis and Ruppia maritima in the flooded ponds. The soils of the periphery were always oxic (Eh>+500mV), but most of the abandoned saline ponds had suboxic (~+100mV<Eh<~+350mV) and even anoxic conditions (Eh<~+100mV), as shown by the existence of gley colours and redoximorphic features. The soil bulk density of the surface and subsurface layers showed that the most impermeable ponds were located in the centre of the marsh, where it is possible to maintain a surface water sheet during prolonged periods, suitable for the development of submerged plant species such as R. maritima and for waterbirds. Part of the seawater poured into more permeable ponds, such as those located in the southern and northern zones of the marsh, is lost by infiltration due to the lower bulk density of these soils. The latter facilitates the recovery of the piezometric levels and the growth of terrestrial plant species. Monitoring of redoximorphic features in the upper soil layers, in combination with symptoms of damage in the plants, could be used as a visual indicator of oxygen limitation due to excessive soil moisture. This would permit the regulation of the irrigation programme, hence optimising the energy and economic resources applied to maintain the ecosystem.