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Abstract Municipal sewage, septic tanks, fertilizers, animal feedlots and irrigation wastewater are the common sources of groundwater pollution in rural areas. Sedimentation pools of wastewater treatment plants are possibly suggested to be another source of pollution. Two wastewater treatment plants located at Qalyubia Governorate named Qalyub (QWTP) and Shubra Al-khayma (SHWTP) were selected to carry out the present study; two samples from influent and effluent were collected seasonally from both plants. Furthermore, 6 groundwater samples were collected from nearby rural houses of both plants. The physicochemical and microbiological properties were evaluated for all samples. Moreover, BOX-PCR for 12 strains isolated from wastewater and groundwater at Qalyub district was carried out. Water quality assessment studies and field observations proved that the seasonal variations had no impact on all sampling sites but 2point source contamination3. The effectiveness of the two wastewater treatment plants under investigation is questionable, especially QWTP. The percentages of removing of TSS, COD, BOD, ammonia, total coliform and faecal coliform counts were 87, 74, 88, 66, 94 and 89%, respectively, for QWTP, and 85, 89, 93, 86, 94 and 83%, respectively, for SHWTP.The groundwater at Qalyub district was contaminated with Mn, Fe, ammonia, BOD, coliform bacteria, faecalstreptococci, E.coli, Aeromonashydrophila and Pseudomonas aeruginosa, while the groundwater at Shubra Al-khayma district was contaminated with Mn, coliform bacteria, faecalstreptococci and P. aeruginosa. Microbial and chemical evaluation of groundwater, as well as, BOX-PCR results confirmed that water treatment plants have no negative impact on the quality of shallow groundwater. To purify the contaminated groundwater with bacteria, a designed filter was suggested |