Lake Qaroun is used as a reservoir for agricultural drainage water via El-Bats and El-Wadi drains. Some physico-chemical parameters and macrobenthic invertebrate community structure were seasonally studied at different stations in the lake during 2014 to 2015. The results revealed that the stations in front of El-Bats and El-Wadi drains suffer from low transparency and decrease of its oxygen content. Moreover, the station in front of El-Bats drain recorded the highest values of the biological oxygen demand (BOD) and phosphates as a result of high amount of discharged organic matter. In addition, the station in front El-Wadi drain revealed the highest concentrations of nitrate, copper and iron. Although the structure of macrobenthos assemblage seems to be complex and influenced by many factors, it was remarkable that the station in front El-Wadi drain had an adverse effect on it. Consequently, continuous and increased pollution by the drainage water contaminated with sewage and heavy metals affected severely most of Lake Qaroun organisms. Therefore, sewage and drainage waste water should be treated before discharging into the lake.