The presence of emerging contaminants like pharmaceuticals in the environment is prompting the search of new methods to concentrate and remove them from soils, sediments and effluents. A completely biocompatible aqueous biphasic system composed of Tween 20 or Tween 80 and the ionic liquid choline chloride has been designed for extracting non-steroidal anti-inflammatory drugs from aqueous streams. After an initial evaluation of the salting out potential of the selected ionic liquid at different temperatures, the extraction capacity of these systems to be applied for ibuprofen and diclofenac removal from aqueous streams was assessed. Very high levels of contaminant removal (higher than 90%) were reached for all the temperature and feed concentrations used. The suitability of the proposed biocompatible aqueous biphasic systems for the treatment of drugs-polluted effluents from surfactant-based soil washing operations is envisaged.