Nitrogen (N) and phosphorus (P) losses to surface and coastal waters are still critically high across Europe and globally. Measures to mitigate and reduce these losses are being implemented both at the cultivated land surface and at the edge-of-fields. Woodchip bioreactors represent a new alternative in Denmark for treating agricultural drainage water, and the present study—based on two years of data from five Danish field-based bioreactors—determined N removal rates varying from 1.49 to 5.37 g N m−3d−1and a mean across all bioreactors and years of 2.90 g N m−3d−1. The loss of phosphorus was relatively high the first year after bioreactor establishment with rates varying from 298.4 to 890.8 mg P m−3d−1, but in the second year, the rates ranged from 12.2 to 77.2 mg P m−3d−1. The investments and the costs of the bioreactors were larger than expected based on Danish standard investments. The cost efficiency analysis found the key issues to be the need for larger investments in the bioreactor itself combined with higher advisory costs. For the four woodchip bioreactors considered in the cost efficiency analysis, the N removal cost was around DKK 350 per kg N ($50 per kg N), which is ca. 50% higher than the standard costs defined by the Danish authorities. Based on the estimated costs of the four bioreactor facilities included in this analysis, a bioreactor is one of the most expensive nitrogen reduction measures compared to other mitigation tools.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10661-023-11358-8.