The present work describes the development and validation of a sensitive method for the determination of traces of diverse groups of pharmaceuticals and endocrine disruptors in surface water. Thirty-seven substances have been selected, including 10 pesticides, 6 hormonal steroids and assimilates, 12 pharmaceuticals, 5 alkylphenols, 1 chlorophenol and 3 other well-known human contaminants, 1 UV filter and 2 plasticisers. An automated online solid-phase extraction (SPE) is directly coupled to liquid chromatography–tandem mass spectrometry. Different SPE columns have been tested, and the injection volume has been optimised. The developed analytical methodology is based on the direct injection of 2.5 mL of water sample acidified at pH 1.6 on an Oasis HLB loading column (20 × 2.1 mm) with 5-µm particles. Then, the chromatographic separation is achieved on a Kinetex XB C18 (100 × 2.1 mm; 1.7 µm) column, and the quantification is realised in multiple-reaction monitoring mode. The online SPE step warrants minimal sample handling, low solvent consumption, high sample throughput, saving time and costs. This method allows the quantification of the target analytes in the lower ng/L concentration range, with limits of quantification (LQs) between 100 pg/L and 10 ng/L, 26 compounds having LQ lower than 1 ng/L. The monitoring of two selected MS/MS transitions for each compound allows the reliable confirmation of positive findings even at the LQ level. The developed and validated methodology has been applied to the analysis of various real samples from two French rivers. Twelve target compounds have been detected in the environmental samples, and the major pollutants are pharmaceuticals usually used by humans (paracetamol, carbamazepine, oxazepam, ketoprofen, trimethoprim). The pesticides atrazine and carbendazim have been ubiquitously detected in real samples too. Metronidazole, sulfamethoxazole and diuron were also frequently quantified in the water samples.