In this paper, a comprehensive study of the fate of an antibiotic, lincomycin, in the aquatic environment is presented. High-resolution mass spectrometry was employed to assess the evolution of the process over time. Formation of intermediate compounds was followed by high performance liquid chromatography-high resolution mass spectrometry (LC-HRMS); accurate mass-to-charge ratios of parent ions were reported with inaccuracy below 1 mmu, which guarantee the correct assignment of their molecular formula in all cases, while their MS(2) and MS(3) spectra showed several structural-diagnostic ions that allowed to characterize the different transformation products (TPs) and to discriminate the isobaric species. The simulation of phototransformation occurring in the aquatic environment and the identification of biotic and abiotic TPs of the pharmaceutical compound were carried out in different experimental conditions: dark experiments, homogeneous photolysis and heterogeneous photocatalysis using titanium dioxide, in order to recreate conditions similar to those found in the environment. Twenty-one main species were identified afterwards lincomycin transformation. Several isomeric species were formed and characterized by analyzing MS and MS(n) spectra and by comparison with parent molecule fragmentation pathways. The major transformation process for lincomycin is hydroxylation either at N-alkyl side chain or at the pyrrolidine moiety. In addition, oxidation/reduction, demethylation or cleavage of pyranose ring occurs. Based on this information and additional assessment of profiles over time of formation/disappearance of each species, it was possible to recognize the transformation pathways followed by the drug.