Triclosan (TRC), chloroxylenol (PCMX) and methylisothiazolinone (MIT) have been commonly used as an antimicrobial in soaps while borax (BRX) is used in household cleaning. After using these chemicals, they are washed down drains and getting into the aquatic ecosystem in which they may affect aquatic living organisms. In the present study, the chronic effects of TRC, PCMX, MIT and BRX on genotoxicity, gene expression and histopathology of rainbow trout (Oncorhynchus mykiss) were evaluated for 40 days under semi static condition. The comet assay results indicated that MIT, TRC and PCMX caused significant DNA damage to erythrocytes of the fish. Transcription of SOD, GPX1, GPX2, GSTA, HSP90BB, HSP90BA, CAT, and HSC70A genes were significantly regulated as a result of TRC, PCMX, MIT, and BRX exposure except PCMX exposed GSTA gene. Histological lesions were detected in gills, spleen liver, and trunk kidney of the fish. Lamellar fusion, hyperplasia and epithelial necrosis in gills, melanomacrophage centers and splenic necrosis in spleen, pyknotic nucleus, fat vacuoles, necrotic hepatocytes in liver, cloudy swelling in the tubules, renal tubule epithelial cells degeneration, glomerular capillaries dilation and glomerulus degeneration in kidney, were observed. Our study demonstrates the chronic toxic effect of TRC, PCMX, MIT, and BRX is high in rainbow trout. Therefore, we should be more careful when using these chemicals for cleaning in order to protect aquatic environment.