The habitat of microorganisms is different from one to another, some are naturally found in water environment, others are introduced due to different sources of contamination. The present study aimed to characterize the bacterial community of diverse water resources in Egypt in relation to the contamination source pursued them. So, water samples were collected from seven different water resources; groundwater, Nile River water, agricultural drainage water (El-Hussieniya drain), sewage contaminated drain (Bahr El-Baqr drain), industrial wastes contaminated drain (Al-Khadrawiya drain), fresh water Lake (Nasser Lake) and brackish water Lake (Qaroun Lake). A total of 2218 bacterial isolates were collected, purified and identified by means of biochemical reactions and 16S rDNA sequence analysis to 21 bacterial genera. The sewage contaminated drain water (Bahr El-Baqr drain) has the highest diverse bacterial community, while the fresh water (Nasser) Lake has the lowest diverse community due to lake of contamination.  In addition, Bacillus, Pseudomonas and Staphyllococcus were the most popular genera, where they have been detected in all types of water resources. The less popular genera were Yersinia, Klebsiella, Aerumonas, Shigella, Salmonella, Cardiobacterium, Arthrobacter and Streptobacillus, where they all have been detected once.