One main reason for the contamination of drinking water and food is the traditional use of untreated wastewater for irrigation purposes. The World Health Organization has therefore compiled standards governing the hygienic quality of irrigation water. However, they can only be attained if raw wastewater is adequately treated. Single-stage planted soil filters usually achieve a reduction in faecal coliform of 2 orders of magnitude. In a joint project, different types of constructed wetland systems were tested in a comparative study addressing sanitisation and other aspects of treatment performance. Initial findings from the first year’s operation of a pilot plant system in Germany indicate that horizontal and vertical flow filters can achieve similar germ reduction. Filter material with a slightly higher hydraulic capacity and larger pore volume proportion impairs the sanitisation performance. There are low indications, that Phragmites australis has no direct influence on the germ reduction performance.