Wet storage of timber and pulpwood produces large quantities of run-off water. A study was conducted to determine the purification efficiency of soil-plant systems for log yard run-off. Sixteen 1200-l lysimeters (1.2 m deep soil columns) with clay or sand soil were planted with willow (Salix sp.) or alder (Alnus glutinosa), and irrigated with run-off from a Norway spruce (Picea abies) log yard. Drainage water was analysed for total organic carbon (TOC), phenols, total P and total N in order to determine concentrations and levels of retention. High retention of TOC, phenols and P occurred in the lysimeters, but no clear differences between willows and alder or clay and sand were identified. Lysimeters with high levels of irrigation showed greater retention than those with low levels. Soil-plant systems using willow and alder could provide an alternative for log yard run-off purification: the key requirement is to optimise irrigation rather than manipulate the plants or soils.