Today, municipal wastewater treatment and disposal environmentally appropriate to the host resources is one of the most essential services. Despite many efforts to do the treatment, again poses threats to aquatic and other consumers due to the use of improper methods of treatment, and the remnants of refined pollutants into rivers. The output wastewater of South Isfahan Wastewater Treatment Plant (SI-WWTP) is discharged into the Zayandehroud River for years, and in addition is used for agriculture in downstream. The Bleach, the wastewater of the Chlor-alkali industry from Isfahan Nirou-Chlor Company) is used in the SI-WWTP, as human sewage treated wastewater disinfectant, since 2012-2013. Finally wastewater of the SI-WWTP with a certain dose of the Bleach enters into the Zayandehroud River. This study was carried out to evaluate the effects of the Bleach on water quality and benthic communities of the Zayandehroud River in three parts, including:1- The effects of the Bleach on the quality of wastewater and river water at the downstream of the IS-WWTP 2-Spatial and temporal changes of biological indices, richness and diversity ndices of benthic macroinvertebratesoh of the river bed, 3- Analyze the effects of the other factors such as discharge and water quality in long term periods (20 years) on the benthic communities. The results of this study showed the Bleach has high efficiency in reducing some parameters such a Fecal coliforms (99.99%), BOD5 (72.6%) and little efficiency in reducing the TSS (17.4%) and TDS (27%). In contrast, measureing the quality parameters in wastewater samples before and after addition of the Bleach, showed increasing trend i many parameters such as the EC, COD, Free chlorine and Total chlorine of wastewater samples after adding the Bleach. Calculation of biological indicies, diversity and water quality indices indicates very poor water quality at the downstream of the IS-WWTP compared with the two upstream stations in October 2015. Comparing the results of diversity indices and BMWP and ASPT in this study with results of the previous studies in 1999, 2004 and 2006 (the years before the use of the Bleach) showed a decrease in benthic communities diversity and remove of some sensitive species in 2015. According to the spatial and temporal changes of the flow and water quality of the river in the last 20 years and their relation to biological parameters of the benthic communities of the river, it can conclude that using of the Bleach a disinfectant have had serious negative effects on benthic communities. Key words : Blaech, Bnthic Macroinvertebrate, Water quality, Wastewatere quality, South Isfahan Wastewater Treatment Plant