This study approach seeks to characterize the hydraulic interactions between the Nile and the Quaternary aquifer via riverbank filtration (RBF) in Abu Tieg area, Assuit Governorate. The substantial removal/reduction of the most problematic substances during percolation of Nile water into abstraction wells was investigated using physico-chemical and biological indicators. Four sites with 11 municipal wells (20–750 m from the Nile) tapping the alluvial aquifer that is fed by the riverbank infiltrate were monitored. Bank-filtrated water was compared with those of the Nile and groundwater. Results showed that infiltrated Nile water ratio into the wells ranged from 39 to 80% reflecting the effect of distance from the Nile. Removal efficiency of total algal, total and faecal coliforms in bank-filtered water was 99.9%, while turbidity removal ranged from 93 to 98%. Fe, Mn and Zn in the bank-filtered water were relatively higher than those in the Nile, but were still under the allowable standards except those of Mn. LSI and WQI for the bank-filtered water indicated that the water was ranked as non-corrosive and of excellent quality. Comparison of physico-chemical and microbiological characteristics of the bank-filtered water with those of the Nile and groundwater showed the high efficiency of RBF as a treatment technology with minimal cost compared to conventional methods.