Pesticide pollution in aquatic ecosystems poses a prevalent and pressing concern, with a particular emphasis on developing nations. The effect of cypermethrin (CP), a synthetic type II pyrethroid pesticide, on phenotypic traits, enzyme activities, and biochemical nutrients in freshwater, mrigal fish (Cirrhinus mrigala) was investigated in this study. Fingerlings were exposed to CP concentrations of 0.0065, 0.013, and 0.026 ppm to determine the median lethal concentration (LC50) for 32 hours and subsequently, three sub-lethal concentrations of 0.0026 ppm, 0.0013 ppm, and 0.00065 ppm were employed to analyze the chronic toxicity stress for 6 weeks. Fish fingerlings tolerated well at lower concentrations (0.0065 ppm) of CP over exposure times, while 50% mortality occurred at 0.13 ppm and 0.026 ppm after 32 hours and 4 hours of exposure, respectively. In the present investigation, growth and eye diameter showed marked differences among treatments, while remaining, total length (TL), standard length (SL), head length (HL), tail length, head width (HW), body depth (BD), body area (BA) and dressing percentage (DP) were found similar among treatments. This study revealed that the amylase and protease activities decreased significantly at increasing concentrations of CP. On the other hand, biochemical nutrients (protein, lipid, moisture, and ash) among the treatments were similar. This study proves that short-time exposure to CP has a negative impact on fish growth and enzymatic activities, however, further studies, such as metabolomic approaches are required to fully explore the effect of CP during sub-lethal exposures.