Silver nanoparticles (AgNPs)-alginate composite beads were synthesized using three different approaches as filler materials of packed columns for simultaneous filtration-disinfection as an alternative portable water treatment process. The prepared composite beads were packed into a column through which Escherichia coli containing water was filtered to evaluate the disinfection efficacy. Excellent disinfection performance (no detectable viable colony) was achieved with a hydraulic retention time (HRT) as short as 1 min (the shortest tested) with the SGR (Simultaneous-Gelation-Reduction) and AR (Adsorption–Reduction) beads that were prepared using in situ reduction of Ag+. Comparatively, the SGR beads released significantly less Ag+/AgNPs than the AR beads did within the same HRT. From the results of this study it was identified that SGR may be the best choice among all three different synthesis approaches in that the SGR beads can achieve satisfactory bactericidal performance with a relatively low material consumption rate.