Determining natural background levels (NBLs) is a fundamental step in assessing the chemical status of groundwater bodies in the EU, as stipulated by the Water Framework and Groundwater Directives. The major challenges in deriving NBLs for trace metals are understanding the interaction of natural and anthropogenic processes and identifying the boundary between pris-tine and polluted groundwater. Thus, the purpose of this paper is to present a roadmap guiding the process of method selection for setting meaningful NBLs of trace metals in groundwater. To de-velop the roadmap, we compared and critically assessed how three methods for excluding polluted sampling points affect the NBLs for As, Cd, Cr, Cu, Ni, and Zn in Danish aquifers. These methods exclude sampling points based on (1) the primary use of the well (or sampling purpose), (2) the dominating anthropogenic pressure in the vicinity of the well, or (3) a combination of pollution indicators (NO3, pesticides, organic micropollutants). Except for Ni, the NBLs derived from the three methods did not differ significantly, indicating that the data pre-selection based on the primary use of the wells is an important step in assuring the removal of anthropogenically influenced points. However, this pre-selection could limit the data representativity with respect to the different groundwater types. The roadmap (a step-by-step guideline) can be used at the national scale in countries with varying data availability.