With water access challenged, there is a need to develop efficient and sustainable alternatives for water purification. Here, cellulose nanofibrils (CNFs) isolated from three source materials (softwood, soybean hulls and oat straw) were compared for the generation of hydrogels beads, using cellulose as support, and reducing agent for silver nanoparticles formation. The silver-functionalized hydrogel beads (Ag-CNFs) were characterized, and the surface energy and specific surface area were evaluated. Antimicrobial testing was conducted to assess the efficacy of the Ag-CNFs against E. coli. The results showed that the Ag-CNFs had a higher specific surface area and lower surface energy compared with unmodified CNFs. Softwood-based Ag-CNFs exhibited the highest silver content and specific surface area, while the soybean hull based showed the highest hydrophobic character. The silver-functionalized soybean hull CNFs (Ag-sbCNF) showed the highest efficacy in reducing the growth of bacteria. Overall, this study highlights the potential of silver-functionalized CNFs hydrogel beads as a promising environmentally friendly and sustainable material for water filtration and disinfection. The findings also suggest that lower surface energy of the Ag-CNFs play an important role in their antimicrobial effect on tested water by enabling shorter retention, providing useful insights into the design of future water filtration materials.