In this study, many findings were observed by monitoring seasonal variations of physical, chemical and microbiological characteristics of raw water of seven main canals used by Water Purification Plants in Kafr El-Sheikh governorate; those findings elucidated the quality of these resources and how would they become affected by pollutants especially during winter season and low demand period of Nile River. This study discussed nitrification process occurrence and how would this process and those characteristics affect each other. These seasonal changes during winter season are affecting and altering physicochemical and microbiological parameters of raw water in a bad way causing many problems especially in drinking water purification plants located on Nile River and main canals. Identification of ammonia oxidation and degradation responsible bacteria revealed that Nitrosomonas europaea and Bacillus amyloliquefaciens were involved in ammonia removal and nitrification process.