In this work, Moroccan surface waters were analysed for 27 endocrine disrupting chemicals and pharmaceutically active compounds. The study area was selected on the grounds of the scarcity of information about the contamination status of rivers in the Rabat region, which receive micropollutants from municipal and industrial wastewater, and runoff from agricultural fields. In fact, animal feed residues, urban water runoff and untreated waste discharges into old landfills reach river water in an area with a population of ca. 3 752 800 where more than 99% of all drinking water is obtained from surface water. Samples were collected at five different sites upstream and downstream the river Bouregreg and the target compounds determined by using a continuous solid-phase extraction system and gas chromatography–mass spectrometry. Unlike the pharmaceuticals, most of the EDCs (specifically, 4-tert-octylphenol, nonylphenol, 4-phenylphenol, 2-phenylphenol, estrone, 17β-estradiol, triclosan and bisphenol A) were present in all samples with detection frequencies above 68%, the highest concentrations (142–368 ng/L) being those at the river mouth. The pharmaceuticals found encompassed five therapeutic classes and their concentrations ranged from 2.5 to 351 ng/L. Overall, the most abundant class were the anti-inflammatory/analgesic drugs with high detection frequencies (80%), followed by antibiotics and anti-epileptics (64%), lipid regulators (56%) and β-blockers (12%). Based on the principal component analysis, the distribution of the emerging contaminants studied among sampling sites was consistent with the physico–chemical properties of the water, the most heavily contaminated sites being those close to the mouth of the river.