The removal of faecal coliforms (FC), Escherichia coli, somatic coliphages and F-specific bacteriophages was monitored over a period of 2 years in two vertical flow constructed wetlands (VFCWs) and four intermittent sand filters (ISFs) that treat pond effluent. Tracer tests (NaCl) were performed to estimate the hydraulic retention time (HRT) of the filters. The contribution of Phragmites australis to the removal of the faecal indicators was examined. The effect of media characteristics (depth, type of sand), hydraulic load and water application schedule on disinfection was also addressed. Planted and non-planted vertical sand filters were equally effective in removing microorganisms. The disinfection capacity was very sensitive to the depth and operation of the filters. HRT was the key parameter regarding filter disinfection capacity. Bacterial indicators were removed at a higher rate than viral ones. Somatic coliphages were removed at higher rates than F-specific bacteriophages.