The increasing demand for herbicides in agricultural fields affected aquatic environments as they entered into water bodies by agricultural runoff. Glyphosate (GLY), an organophosphate herbicide, is widely used in India for weed control. This study aimed to evaluate the toxic effects of GLY on climbing perch Anabas testudineus by studying its effects on the gonadosomatic index (GSI), hepatosomatic index (HSI), gonad and liver histology, spawning performance, and haematological parameters (RBC, WBC, haemoglobin). In this study, Anabas testudineus were exposed to three sub‐lethal concentrations of GLY such as T1: 2.6 ppm (1/30th of 48h LC50), T2: 3.9 ppm (1/20th of 48h LC50) and T3: 7.8 ppm (1/10th of 48 hr LC50) for 45 days with 12 fish in each tank. Results indicated a significant decrease in GSI, HSI, structural alterations in testis, and ovary on 30th and 45th days of exposure. Vacuolation in tissue, dilution of sinusoid, altered tissue architecture in the liver, reduction in spawning performances (fertilization and hatching rate), increase in WBC count, decrease in RBC number and haemoglobin content were observed in all treatment groups on the 45th day exposure. Thus, the outcome of the present study revealed that the herbicide could deleteriously impair reproductive fitness, alter the liver structure, and haematological parameter of A. testudineus with a possible reduction in growth and population size.