Chlorine is a widely used water disinfectant, while fluoride is an element which is naturally found in water or artificially added to it. Many regulations have been set to monitor the quality of water and ensure its safety. Chlorine and fluoride have many toxic effects if their levels exceeded the allowed levels. This work aimed estimation of levels of chlorine and fluoride in drinking water of Benha city and study their chronic toxic effects on adult male albino rats. Method: collecting water samples from urban areas, rural areas and bottled water then estimate levels of chlorine and fluoride. Seventy adult male albino rats were divided as follows: control group (10 rats), chlorine groups (30 rats which have been subdivided into three groups received different doses of chlorine for eight weeks). Fluoride groups (30 rats which have been subdivided into three groups received different doses of fluoride for eight weeks). The results of present study revealed the followings: Chlorine levels in urban area were above the allowed recommended levels, while its levels in rural areas were within the allowed level .Fluoride levels in urban areas, rural areas and bottled water were below the recommended doses. A decrease in body weight in all treated group have been observed; histopathological changes in (liver, kidney, urinary bladder and large intestine) have been observed and these changes were dose dependent. We recommended adjusting level of chlorine in both rural and urban areas to follow the world health organization recommended levels. Fluoridation programs also should be applied in Benha to cover up the low level in water.