The aim of this study was to detect and quantify the level of emerging contaminants in the groundwater of the Fuente de Piedra salt lake endorheic basin located in the Málaga province (Southern Spain). The Fuente de Piedra salt lake is an area of ecological importance due to its location, geology, hydrogeology and climate. For this reason, in 1983 it was declared as a RAMSAR site and in 1984 it was declared as a Natural Reserve. Later, in 1988 it was declared as an Important Bird and Biodiversity Area (IBA) and still is to this day. A sampling campaign was carried out to extract the groundwater samples from the study area. The sampling network consisted of 22 points distributed all over the basin. The emerging contaminants analysis was carried out in the Research Services of the Institute of Marine Research (INMAR) in University of Cadiz (Spain). To this end, Gas Chromatography-Mass Spectrometry (GC/MS) after stir bar sorptive extraction (SBSE) was used in order to determine the targed compounds in the groundwater samples. Results confirm the presence of a wide range of targed compounds. However, unusually high concentrations of endocrine disruptors such as 17-α-ethinylestradiol (9-670 ppt), 17-β-estradiol (27-712 ppt) and Nonylphenol (1-67 ppt) were found. To our knowledge, it is the first time that such high concentrations of these chemicals have been detected in groundwater. Additionally, the ecotoxicological risk of endocrine disruptors was estimated using their risk quotients. The findings suggest that there is a significant ecological risk for green algae species but not for Daphnia or fish. Nonetheless, biomagnification of these compounds in the food chain could be a concern for other species living at this environment. Further epidemiological and toxicity studies are needed.