To investigate transport processes in soils, detailed information about the spatial distribution of solutes is required. We describe a method to obtain concentration maps of fluorescent tracers on cross sections of soil cores with a high spatial resolution. The fluorescence signal of two dye tracers, brilliant sulfaflavine (BF; 1H‐Benz(de)isoquinoline‐5‐sulfonic acid, 2,3‐dihydro‐6‐amino‐1,3‐dioxo‐2‐(p‐tolyl)‐, monosodium salt) and sulforhodamine B (SB; xanthylium, 3,6‐bis(diethylamino)‐9‐(2,4‐disulfophenyl)‐, inner salt, sodium salt), was imaged on the exposed cross sections. The fluorescence signal was corrected for variable illumination light intensity and optical properties of the soil across the exposed surface. Correction factors for varying optical soil properties were derived from the image of the reflected excitation light at the exposed surface. Linear calibration relations related the corrected fluorescence image to the total tracer concentration (Ct) map, that is, mass of dye dissolved in the soil solution and sorbed to the soil particles per unit volume bulk soil. Corrections for varying optical properties of the soil surface were important to reduce the uncertainty of the concentration that was estimated from the fluorescence signal. For BF, the calibration relations were different for different soil materials and a soil specific calibration had to be used. Variations in background fluorescence were an important source of uncertainty of the BF concentration estimates but can be overcome by applying higher concentrations. For SB, variations in calibration relations and in the background fluorescence were considerably smaller, and so is the uncertainty of the estimated SB concentrations.