Tourism is one of the most important activities for the economy of Nor Patagonia Argentina. In Bariloche City, located on the shores of Lake Nahuel Huapi, both the permanent and the temporary populations have increased significantly in recent decades, and this has not necessarily been accompanied by an improvement in sewage networks. Emerging micropollutants such as pharmaceutical compounds reach aquatic systems directly, in the absence of a domestic sewage network, or through effluents from wastewater treatment plants (WWTP), which do not efficiently remove these substances and represent a major threat to the environment. Therefore, the objective of our study was to monitor the presence of pharmaceutical compounds discharged both through wastewater effluents and diffusely from housing developments into Lake Nahuel Huapi. The results obtained demonstrate the presence of pharmaceuticals in Lake Nahuel Huapi with concentrations ranging from not detectable (ND) to 110.6 ng L–1 (caffeine). The highest pharmaceutical concentration recorded in WWTP influent corresponded to caffeine (41728 ng L–1), and the lowest concentration was paracetamol (18.8 ng L–1). The removal efficiency of pharmaceuticals in the WWTP was calculated, and ranged from 0% for carbamazepine to 66% for ciprofloxacin. This antibiotic showed the lowest % of attenuation (73%) in Lake Nahuel Huapi. These results on the occurrence of a wide variety of pharmaceuticals are the first generated in Patagonia, representing a regional baseline for this type of micropollutant and valuable information for the subsequent design of removal strategies for emerging pharmaceutical pollutants in surface water. Environ Toxicol Chem 2024;00:1–11. © 2024 SETAC