"Advanced" pond systems (APS) have the potential for improving treatment, including disinfection, over conventional WSPs. Disinfection in a pilot scale APS at Ngatea, New Zealand was studied. This system comprises a high-rate algal pond (HRP) that optimises growth of settleable colonial green algae, followed by an algal settling pond (ASP) that removes much of the nutrients and solids as non-noxious algal sludge, and then a maturation pond (MP) for effluent polishing. Monitoring of this pilot-scale system over 2 years showed excellent overall removal of E. coli (average of 2000-fold reduction), with approximately 1 log removal in each of the three stages. Experiments in the pilot scale HRP suggest that most E. coli removal in this stage is inactivation by sunlight exposure, but with an important contribution from continuous dark processes. Preliminary experiments on the pilot scale algal settling pond (APS) suggest the combined effect of sedimentation of bacteria and sunlight disinfection of the (clarified) supernatant water.