Typical methods of doping quantification are based on spectroscopy or conductivity measurements. The spatial dopant distribution assessment with nanometer-scale precision is limited usually to one or two dimensions. Here we demonstrate an approach to detect three-dimensional dopant homogeneity in GaN:Si layers using electrochemical etching (ECE). GaN:Si layers are grown by plasma-assisted molecular beam epitaxy. Dopant incorporation is uniform when the growth front morphology is atomically flat. Non-uniform Si incorporation into GaN is observed when step-bunches are present on the surface during epitaxy. In this study we show that local Si concentration in the area of step-bunch is about three times higher than in the area between step-bunches. ECE spatial resolution in our experiment is estimated to be about 50 nm. This makes ECE a simple and quantitative probing tool for local three-dimensional conductivity homogeneity assessment. Our study proves that ECE could be important both for fundamental studies of crystal growth physics and impurity incorporation and for ion-implanted structures and post-processing device control.