Field, drillcore and geochemical data are used to create a three-dimensional implicit model to assess the controls on gold mineralization at the Nalunaq orogenic gold deposit in South Greenland. Gold occurs in narrow quartz veins with variable dips averaging 34° SE that cut meta-basic rocks. The bulk of the mineralization is contained within a single gold–quartz vein, named the Main Vein. Within this vein, gold is concentrated into three ore shoots plunging 20–25° NE, corresponding to the South, Target and Mountain blocks of the Nalunaq gold mine. Gold anomalies in drillcores are identified updip and downdip from the current mine workings. Modelling reveals that structural controls have the greatest influence on the location of gold. Flexures in the Main Vein correspond to changes in the host rock lithology and the gold grade is highest where the quartz vein is steepest. Where late-stage faults intercept the Main Vein, gold grades are lower. The comprehensive gold assay data from the mine, which are integrated with structural observations in the implicit model, refine the structural interpretation of the Nalunaq gold deposit, highlighting the ore shoot geometry and delineating the minimum extents of mineralization beyond the currently mined areas.