Fish health can be affected by a multitude of stressors. Acute and chronic stress assessment via specific hormones monitoring has become a trending research topic. Common investigated matrices are blood and plasma, but recently less invasive substrates have been identified. As chemical composition of skin mucus/epidermis has been demonstrated to link with acute stress, and of scales with chronic stress in fish, the aim of the study was firstly to improve the determination of three stress hormones, namely cortisol (COL), cortisone (CON), and dehydroepiandrosterone-3-sulfate (DHEAS), in skin mucus/epidermis and scales of Aphanius fasciatus. Secondly, an evaluation of the impact of different environments on hormones concentrations was carried out. A liquid chromatography coupled to tandem mass spectrometry method (HPLC-MS/MS) and a preanalytical procedure were validated to determine COL, CON and DHEAS. This methodology was applied to compare a pull of field-collected fish with a pull of fish housed in the laboratory for one year. Our results highlighted a significant presence of cortisol and cortisone in epidermis of the latter pull (averagely 0.10 and 0.14 ng mg−1, respectively), while in the first pull both hormones were much less concentrated (averagely 0.006 and 0.008 ng mg−1, respectively). Scales of both pulls showed presence of hormones, with a higher concentration for fish housed in the laboratory, although a relevant difference in concentration was found only for cortisone. DHEAS was always below the limit of detection.