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Abstract Background Textile dyes which are eliminated as unfixed dyes through the effluent from textile industry cause deleterious effect on the fresh water fish. Thus, toxicity tests were conducted using indigo dye on Oreochromis niloticus juveniles (mean weight 30.00 ± 0.73 g) as a test fish under bioassay system. Varying concentration of 0.00 (control), 0.5, 1.0, 1.5, 2.0, and 2.5 mg/l containing graded levels of Indigofera were applied in experimental tanks to determine the lethal concentration. The LC50 of dye at 96 h was 1.3 mg/l of water. The histopathology (heart, gills, kidney and spleen) and water quality parameters (Dissolved oxygen, pH and temperature) were determined using standard methods and behavioural responses were observed. Results Histopathology of heart, gills, kidney and spleen revealed degeneration of cells, space formation, slight cellular changes and vacuolation among the treatments especially in the higher concentration of 1.5 mg/l, 2.0 mg/l, and 2.5 mg/l of the dye solution used except in the control. The pH and DO of control were significantly different from the experimental units while there was no significant variation in the temperature of the control and all the experimental units. Effects of indigo dye on water parameters were significant (P |