The present work evaluates the effect of contact filtration, preceded by coagulation with zirconium (Zr) and chitosan coagulants, on model microorganisms and waterborne pathogens. River water intended for potable water production was spiked with MS2 and Salmonella Typhimurium 28B bacteriophages, Escherichia coli, and Cryptosporidium parvum oocysts prior to coagulation. The hygienic performance demonstrated by Zr comprised 3.0–4.0 log10 removal of viruses and 5.0–6.0 log10 removal of E. coli and C. parvum oocysts. Treatment with chitosan resulted in a removal of 2.5–3.0 log10 of viruses and parasites, and 4.5–5.0 log10 of bacteria. A reference coagulant, polyaluminium chloride (PACl), gave a 2.5–3.0 log10 removal of viruses and 4.5 log10 of E. coli. These results indicate that both Zr and chitosan enable adequate removal of microorganisms from surface water. The present study also attempts to assess removal rates of the selected microorganisms with regard to their size and surface properties. The isoelectric point of the Salmonella Typhimurium 28B bacteriophage is reported for the first time. The retention of the selected microorganisms in the filter bed appeared to have some correlation with their size, but the effect of the charge remained unclear.