Pesticides have become an integral part of agricultural crop production for growing more food. However, the excessive use of pesticides ultimately reaches the aquatic ecosystems and demonstrates pernicious impacts on non‐target aquatic organisms, including fish. Hence, the current study aimed at unravelling the chronic toxicity of an organophosphate insecticide, chlorpyrifos (CPF), on a battery of blood biomarkers, somatic indices and histopathological aberrations of liver and kidney in banded gourami ( Trichogaster fasciata ). Fish were subjected to different sub‐lethal concentrations (0, 15, 50, 150 and 500 µg/L) of CPF for 75 days, and sampling was done at each 15‐day interval. Results indicated a significant rise ( p < 0.05) in glucose, white blood cell levels, mean corpuscular volume and mean corpuscular haemoglobin, and a subsequent decrease in haemoglobin, red blood cell count and packed cell volume. Hepatosomatic index exhibited an increasing pattern, whereas the kidney somatic index followed the opposite trend. Vacuolation, fatty degeneration, dilation of sinusoids and haemorrhage were evident in the liver, whereas kidney histopathology revealed occlusion of the tubular lumen, widened intertubular space, vacuolation, melanomacrophage centre and haemorrhage. Overall, chronic CPF exposure exerted concentration‐ and time‐dependent alterations resulting in anaemia, hepatotoxicity and nephrotoxicity in banded gourami. However, more in‐depth studies are required to understand the changes in fish at the molecular level, such as oxidative stress, gene expression, metabolomic profiling and so forth. The study encourages research for pesticide alternatives and interdisciplinary actions to conserve the aquatic environment as well as the aquatic biota.