Background: Deep rooting is one of the most promising plant traits for improving crop yield under water-limited conditions. Most root phenotyping methods are designed for laboratory-grown plants, typically measuring very young plants not grown in soil and not allowing full development of the root system. Results: This study introduced the ¹⁵N tracer method to detect genotypic variations of deep rooting and N uptake, and to support the minirhizotron method. The method was tested in a new semifield phenotyping facility on two genotypes of winter wheat, seven genotypes of spring barley and four genotypes of ryegrass grown along a drought stress gradient in four individual experiments. The ¹⁵N labeled fertilizer was applied at increasing soil depths from 0.4 to 1.8 m or from 0.7 to 2.8 m through a subsurface tracer supply system, and sampling of aboveground biomass was conducted to measure the ¹⁵N uptake. The results confirm that the ¹⁵N labeling system could identify the approximate extension of the root system. The results of ¹⁵N labeling as well as root measurements made by minirhizotrons showed rather high variation. However, in the spring barley experiment, we did find correlations between root observations and ¹⁵N uptake from the deepest part of the root zone. The labeled crop rows mostly had significantly higher ¹⁵N enrichment than their neighbor rows. Conclusion: We concluded that the ¹⁵N tracer method is promising as a future method for deep root phenotyping because the method will be used for phenotyping for deep root function rather than deep root growth. With some modifications to the injection principle and sampling process to reduce measurement variability, we suggest that the ¹⁵N tracer method may be a useful tool for deep root phenotyping. The results demonstrated that the minirhizotrons observed roots of the tested rows rather than their neighboring rows.