Imidacloprid (IMI), a systemic neonicotinoid insecticide widely used in worldwide scale, is reported in freshwater bodies. Nevertheless, there is a lack of information about IMI sublethal effects on freshwater fish. Thus, the aim of this study was to identify the potential hazard of this insecticide to the South American fish Prochilodus lineatus exposed for 120 h to four IMI concentrations (1.25, 12.5, 125, and 1250 μg L−1). A set of biochemical, genotoxic and physiological biomarkers were evaluated in different organs of the fish. IMI exposure induced significant changes in the enzymatic profiles of P. lineatus, with alterations in the activity of biotransformation and antioxidant enzymes in different tissues. Redox balance of the tissues was affected, since oxidative damage such as lipoperoxidation (LPO) and protein carbonylation (PCC) were evidenced in the liver, gills, kidney and brain of fish exposed to different IMI concentrations. Fish exposed to all IMI concentrations showed decreased blood glucose indicating an increase of energetic demand. DNA damage was evidenced by the comet test, in the erythrocytes of fish all the concentrations evaluated. We integrated these results in the Integrated Biomarker Response (IBR) index, which evidenced that the organs most affected by IMI exposure were the liver and kidney, followed by the gills. Our results highlight the importance of investigating different target tissues after IMI exposure and show the sublethal effects of IMI in some of them; they also warn to the possible consequences that fish living in freshwater ecosystems can suffer due to IMI exposure.