The excessive use of pesticides at different stages of crop production can pose a great danger to the aquatic environment, and particularly to fish. The purpose of the present work was to assess the negative effects of chlorpyrifos (CPF) on the liver histological architecture and the activities of marker enzymes in common carp (Cyprinus carpio Linnaeus, 1758), by applying a multi-biomarker technique. The tested insecticide is categorized as a priority pollutant in surface waters in terms of Directive 2013/39/EU. The carps were exposed to different and environmentally relevant CPF concentrations for 72 h (a short-term acute experiment). The results showed that the tested insecticide alters the liver histological structure, causing degenerative lesions, such as granular and vacuolar degeneration; necrobiotic alterations and necrosis, as well as changes in the circulatory system. In addition, CPF induces changes in the enzymatic activity of lactate dehydrogenase (LDH), aspartate aminotransferase (ASAT), alanine aminotransferase (ALAT), cholinesterase (ChE), glutathione peroxidase (GPx) and catalase (CAT). The results from such experimental set ups could be successfully used in the legislation related to the protection of water bodies from contamination, in areas with intensive application of plant protection products used in agricultural practices, and also in implementing the Water Frame Directive by using multi-biomarker approaches.