For ensuring complete, high-throughput disinfection of water, superior interaction of silver nanoparticles (Ag-NPs) with contaminating E. coli cells in water is crucial. This is achieved by preferential attachment of Ag-NPs on the outer surface of activated carbon (AC), by either plasma or acid treated AC samples, termed as Ag-p-AC and Ag-a-AC hybrids, respectively. In subsequent flow-column experiments, Ag-a-AC showed 4 log reduction in E. coli cells in only 14 min of residence-time, which is much less compared to Ag-p-AC (23 min). This enhanced performance is due to (i) attachment of more Ag-NPs on the outer surface of Ag-a-AC, providing better dispersion of individual Ag-NPs and (ii) altered surface topography of acid-treated AC, due to its higher surface roughness (increasing from 15.29 pm to 1.15 nm on acid treatment). The latter leads to release of more Ag+ ions and, therefore, faster E. coli death in flow-column. Furthermore, Ag-NPs were much more strongly bonded to acid treated AC (944 kJ/mol adsorption energy), compared to plasma treated AC (667 kJ/mol), ensuring no Ag-NP detachment from Ag-a-AC surface during its use. Therefore, acid treatment is an efficient surface modification technique to continuously produce potable quality water at a high throughput of 2.66 L/h, presently demonstrated at least over 5 days.