Aims: High rate algal ponds (HRAPs) have been suggested as replacements for waste stabilization ponds (WSPs) in Community Wastewater Management Systems (CWMS) used in rural South Australian (SA) towns. Treated effluent from CWMS is reused for irrigation. To manage the risk of human exposure to pathogens, the disinfection performance of HRAPs was validated using the common indicators Escherichia coli and F-RNA bacteriophage; aerobic spore-forming bacteria (ASFB) were used as indicators for protozoa. Methods and Results: Using standard culture methods, the removal of the indicator organisms F-RNA bacteriophage, E. coli and ASFB by a HRAP at Kingston-on-Murray, SA, was measured. The mean log10 reduction values achieved for the F-RNA bacteriophage was 1·59 ± 0·82 log10 PFU 100 ml−1 and for E. coli it was 2·13 ± 0·55 log10 E. coli MPN 100 ml−1. ASFB numbers in the treated pond effluent often exceeded those of the influent. Conclusions: The results show that HRAPs are able to remove viral and bacterial indicators to levels acceptable for subsurface irrigation of nonfood crops. Additionally, it was concluded that alternate environmental sources and the potential for regrowth made ASFB unsuitable indicators for pathogenic protozoa in natural pond systems. Significance and Impact of the Study: This study shows HRAPs would be suitable replacements for WSPs in CWMS schemes in regard to pathogen disinfection. Such demonstration of the treatment efficacy of HRAPs, together with their smaller land area requirements relative to WSPs, should facilitate their wider adoption in rural and remote communities.