The long-term use of a filter-based, on-site wastewater treatment system increases nutrient discharge to receiving waters and may reduce its hygienic barrier efficiency. The main purpose of this research was to assess the hygienic barrier efficiency and the associated health risks of an on-site system that had exceeded its 5-yr design capacity with respect to phosphorus (P) removal. The system was investigated for bacteria and virus removal and assessed with respect to potential health risks in relation to reuse of effluent for irrigation. The system consists of a septic tank, a pressure-dosed vertical flow biofilter, and an up-flow filter unit with lightweight clay aggregates. The total P concentration in the effluent had increased gradually from initially <0.1 mg P L(-1) during the first 2 yr of operation to 1.8 mg P L(-1) after 5.3 yr. Escherichia coli was used as an indicator organism for fecal bacteria removal, whereas bacteriophages phiX174 and Salmonella typhimurium phage 28B (S.t. 28B) were used to model enteric virus removal. An overall decrease in E. coli removal occurred from a complete (approximately 5.6 log10) reduction during the first 3 yr of operation to 2.6 log10 reduction. The removal amounts of the bacteriophages phiX174 and S.t. 28B were 3.9 and 3.7 log10, respectively. Based on removal of S.t. 28B, the risks of rotavirus infection and disease for the investigated scenarios were above the acceptable level of 10(-4) and 10(-3), respectively, as defined by the World Health Organization.