Repeatedly deposition of anthropogenic chemicals such as chlorpyrifos led to the risk of its associated unwanted toxicity to the non-targeted organisms. The present project was designed to assess the toxicity of chlorpyrifos, an organophosphorus insecticide, at different dose level and duration of exposure to elucidate its cellular and nuclear anomalies in erythrocytes and histopathological effect on brain and liver tissues of the fresh water fish (Ctenopharyngodon idella). The chlorpyrifos was used at 0.01 and 0.015 μL/L for a duration of 3, 6, 9, 12, and 15 days respectively. Alteration in functional markers such as cellular anomalies associated with exposed dosage was reported as swollen cells, swollen or enlarged cells, and hemolyzed cells followed by nuclear abnormalities stated as micronucleus, deformed nucleus and nuclear shift. The result indicated alterations observed in brain and liver tissues were categorized as necrosis, vacuolization, degeneration of neurons and hepatic necrosis, hepatolysis and hepatic vacuolization that were further scored on the basis of severity from 0 (normal) to 3 (severe). These effects significantly increased with the increase in dose level of chlorpyrifos and duration of exposure (p < 0.05). The present findings contributed that extended exposure of such chemicals to the aquatic ecosystems led to behavioral and histopathological alterations that may result in loss of normal functioning of the organs.