Waste stabilisation ponds (WSPs) are widely used in New Zealand for the treatment of domestic sewage and other organic wastes. Traditionally, faecal coliforms have been used as the faecal indicator in WSPs and their receiving waters but there is increasing interest in alternative indicators. We studied the comparative inactivation kinetics under sunlight of two bacterial indicators in WSP effluent, and also those of two F-specific bacteriophages that may be models of the behaviour of viral pathogens in WSPs. We investigated the wavelength-dependence of sunlight inactivation in rapidly-stirred, small reactors, with temperature, dissolved oxygen and pH control, using various plastics as “longpass” filters to screen different portions of the UV-visible spectrum. The UVB, UVA and blue-green visible radiation (E. coli and presumed FDNA phage were inactivated mainly by UVB, consistent with direct absorption by, and damage to, the DNA with minor or negligible contribution by longer wavelengths. Our results suggest that E. coli may be a better bacterial indicator in WSPs than enterococci.