The presence of pollutants and their transformation products (TPs) in the water system is a big concern because of possible adverse effects on the aquatic environment. Their identification is still a challenge that requires the combination of different chromatographic techniques. In the current research, serial coupling of RPLC and zwitterionic hydrophilic interaction LC with TOF-MS was investigated as a single separation technique for the screening of suspected TPs from electrochemical oxidation of diclofenac using a boron-doped diamond electrode. Diclofenac oxidation was performed in three water matrices in order to study its transformation in different chemical contexts. 47 TPs resulting from similar oxidation methods were selected from the literature. As in most cases standards were not available, an identification procedure based on accurate mass data and chromatographic behavior was proposed. According to this procedure, 11 suspected TPs, previously analyzed by LC, GC, or ion chromatography, were detected in a single injection. The method was proved to be reliable and versatile and it could be efficiently employed as a comprehensive analytical tool for the simultaneous analysis of compounds in a wide polarity range.