This study was carried out in two water treatment plants in Menoufia province (Shebin-Elkom conventional plant and Kafr-Rabeea direct filtration plant to monitor the water quality (physical, chemical and microbiological) beside cyst prevalence of two intestinal parasitic protozoa (Giardia and Entamoeba spp.). It was proved that the highest values of most physic- chemical parameters at Shebin- Elkom and Kafr-Rabeea plants are detected during autumn and winter throughout the various stages.
Samples of raw water at both water treatment plants were positive for total and fecal coliform. Following stages in Shebin-Elkom conventional treatment plant were free from both total and fecal coliforms, while filtrated and potable water samples of Kafr –Rabeea plant showed positive results for these coliform types. This may be due to the failure of the treatment and disinfection process using chlorine. Also, coliform presence in outlet samples may be due to failure of sand filter stage to remove pathogenic organisms, or due to shortage of chlorine below minimum level. Coliform bacteria in the distribution system can be attributed to leaking pipes, valves, joints and seals as well as contamination of the tap by the final consumers.  
            In Shebin-Elkom water  plant  cysts of Giardia and Entamoeba were persisted during the study period in raw water and  reached maximum densities during Summer and completely absent in treated, filtrated and potable water samples which may be due to the complete treatment process and the effect of chlorination during disinfection process. Those of Kafr –Rabeea water plant showed  that Giardia and Entamoeba cysts were persisted all over the study period in raw , filtrated  and potable water samples, and attained maximum densities during Spring and Summer . This may be attributed to failure of sand filters stage to remove cysts and   to insufficiency disinfection process with chlorine.
            Finally, there is a need for a new technology that more effective in water disinfection process such as using solar energy. A preliminary study followed this paper proved that both solar radiation and heat of applying SODIS method have a synergistic effect in destroying cysts of Giardia and Entamoeba spp.