Demographic and socioeconomic pressures resulted in increase of agricultural production, which in turn led to increase in nitrate pollution to groundwater. Biotechnologies create an opportunity to boost the efficiency of groundwater treatment at the ecosystem scale. The aim of the study was to build an underground denitrifying barrier around the manure storing place composed of organic material and to monitor its effectiveness. It was constructed by burying pine sawdust mixes with soil perpendicular to groundwater flow. The preliminary groundwater monitoring gave the average concentration of Ntot equal to 704 mg dm-3, NO3–N equal to 228 mg dm-3and NH4–N to 347 mg dm-3. Preliminary results showed nearly 90% reduction of all forms of nitrogen. The applied technology seems to be an inexpensive tool for diminishing nitrate loads into surface waters and for achieving good ecological status of the entire catchment, as required by the Water Framework Directive.