| Summary: | The Guadiana River is the fourth longest river in Europe and is a natural frontier between southern Portugal and Spain. This river was historically used to transport minerals exploited in the region since the Roman Empire and therefore suffered human interventions that have been intensified after the industrial revolution. The Guadiana River has in its limits the Guadiana Valley Natural Park, which is of great value for the Conservation of Geobiodiversity. This study mainly aims to identify zones with the environmental characteristics in the estuarine area of the Guadiana River based on the distribution and ecology of microorganisms (ostracods and foraminifera) associated with physicochemical parameters and sedimentological and geochemical (carbohydrate, lipid, protein, total organic carbon and total sulfur) data. Fifty-five foraminifera taxa were identified along the estuary with dominance of Ammonia tepida and Miliammina fusca and 13 ostracods taxa with dominance Leptocythere lacertosa and Loxoconcha elliptica. Detrended correspondence analysis (DCA) performed using biotic and abiotic variables indicated that pH, grain size, total organic carbon (TOC) and lipids were the most influent factors in the distribution of these organisms. Four zones were identified in the Guadiana River estuary: i) Low estuary - region with the largest marine influence with sandy sediment, higher salinity and total sulfur and mainly represented by the dominance of estuarine species of foraminifera (Ammonia tepida and Cribroelphidium vadescens) and by the ostracods (Darwinula stevensoni, Semicytherura sulcata and Urocythereis oblonga); ii) Intermediate estuary - region characterized by neutral pH and sandy sediment enriched in carbohydrates; this region is characterized by the presence of the ostracods species Cytherois fischeri and Neocytherideis subulata and by calcareous and agglutinated species in foraminiferal assemblages; iii) Upper estuary - silt, high TOC, proteins and lipids content, and by the presence of Loxoconcha elliptica; iv) Freshwater environment - has similar characteristics to the upper estuary, but do not display foraminifera and was composed of ostracod species such as Cyclocypris ovum, Heterocypris incongruens and Ilyocypris sp. These species are commonly found in freshwater environments or in waters with very low salinity. The predetermined limit in previous studies for the intermediate/upper estuary shifted approximately 5 km further north. This effect may be due to human influence, since a dam was built on the river decreasing the freshwater flow and allowing marine water entrance to an inner area of the estuary.
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