Abstract: Soil salinization and eutrophication are two major threats of soil degradation in the Mediterranean basin, which may have a large impact in the functioning of Mediterranean forest systems. Cork oak forests at Doñana National Park (SW Spain) are affected by soil salinisation and eutrophication, due to the presence of large colonies of wading birds, which supply the soil with high amounts of detritus, resulting in a decline in tree health status. We analysed soil physico-chemical properties, microbial activity (biomass and basal respiration) and composition (T-RFLP: terminal restriction fragment length polymorphisms) of soil microbial communities along a bird influence gradient in these declining forests during two contrasting seasons (autumn and summer). Bird influence resulted in remarkable alterations in the physico-chemical properties of the soil, particularly in increased salinity, and increases in available soil phosphorus, nitrate, ammonium and dissolved organic carbon (DOC). In contrast to our expectations, microbial biomass and respiration increased in those saline soils, due to increases in DOC promoting microbial growth. Increased soil phosphorus had some influence on soil fungal diversity both in autumn and summer, while bacterial communities were only affected by guano deposition in the summer season. Bacterial richness and diversity decreased along the avian intensity gradient in the dry season, while archaeal diversity increased. In conclusion, the presence of large colonies of wading birds at Doñana National Park clearly influences biogeochemical cycles in this declining ecosystem, which obligates to a greater consideration of soil processes in conservation priorities.