The aim of the work was to develop a new HPLC-MS/MS method that allows for the simultaneous detection of antimicrobials agents (targeted analysis) and their transformation products (non-targeted analysis), which enabled the elucidation of their transformation pathways in the environment. Targeted analysis was performed for 16 selected antimicrobials agents (AMs) in wastewater collected at different stages of the treatment process and river water from sections before and after wastewater discharge. The samples were collected in the Łyna sewage treatment plant (Olsztyn, Poland) in three measuring periods at different seasons. Analytes were selected from tetracyclines, fluoroquinolones, β-lactams, macrolides, glycopeptides, lincosamides and synthetic antibiotics.As a part of the targeted analysis, 13 AMs were detected in wastewater samples, and 7 of them in river water samples. However, their presence and concentrations were closely related to the type of the sample and the season in which the sample was taken. The highest concentrations of AMs were detected in samples collected in September (max. 1643.7 ng L−1 TRI), while the lowest AMs concentrations were found in samples collected in June (max. 136.1 ng L−1 CLR). The total content of AMs in untreated wastewater was in the range of 1.42–1644 ng L−1, while in the river water was for upstream 1.22–48.73 ng L−1 and for downstream 2.24–149 ng L−1. In the non-target analysis, 33 degradation products of the selected AMs were identified, and the transformation pathways of their degradation were speculated. In the course of the research, it was found that as a result of the processes taking place in wastewater treatment plant, the parent substances are transformed into a number of stable transformation products. Transformation products resulted from hydroxylation, ring opening, oxidation, methylation or demethylation, carboxylation, or cleavage of the CN bond of the parent AMs.