Raw water resources in Kafr El-Sheikh Governorate are affected by many contaminants particularly during the winter season and low demand period of the Nile River, in which water level decreases and organic matter increases resulting in decreased dissolved oxygen, and increased ammonia, nitrite and bacterial load in the water. In this study, physicochemical and microbiological characteristics of water samples taken seasonally from selected sampling sites on seven main canals in Kafr El-Sheikh Governorate were tested and studied to monitor nitrification process occurrence and study its effect on water quality. The main results of the study included turbidity, conductivity, ammonia, nitrite and nitrate and showed increased values during the winter season. Heavy metals levels showed that iron increased in winter and aluminum increased in spring, while copper increased in winter and spring seasons. Total bacterial count, total coliform and algal count increased in the winter season. Activity of ammonia oxidizing bacteria also increased markedly during the winter season which could be explained by increased ammonia concentration during the same period which enhanced nitrification process occurrence. This study proved that nitrification in environments which provide unfavorable conditions for autotrophic nitrifying bacteria may result from the activity of heterotrophic microorganisms; Bacillus amyloliquefaciens was isolated and identified to be involved.