This research is aimed at elucidating the removal mechanisms of nutrients due to natural attenuation in drainage canals in Evrotas River delta in Greece. We investigated nutrients fluxes in groundwater, sediments, and reeds (Phragmites Australis and Arundo Donax) of the drainage canal. Groundwater fluxes indicated that the rate of mineralization was 37.6 mg N/m(2) day. The accumulation of toxic ammonia was prevented through the nitrification process (26.6 mg N m(-2) day(-1)). The decrease of NO(3)-N flux in groundwater in the riparian zone was calculated to be 56.1 mg N m(-2) day(-1) (20.48 g N m(-2) year(-1)). Phosphate was adsorbed to sediments and its load to the drainage canal was minimized. Harvesting of above ground reed biomass in mid June, when maximum standing stock of nutrients was attained for both plants, would remove 2.73 g P m(-2) and 11.2 g N m(-2). All the phosphorous (1.39 g P/m(2) year(-1)) and 76.5% of the nitrate nitrogen (14.64 g N m(-2) year(-1)) entering the drainage canal was taken up by plants. Drainage canal management is suggested as an efficient low cost-high gain agri-environmental measure, which is easy to be adapted by farmers, to reduce diffuse nutrient pollution.