The virtual lysimeter concept was tested in comparison with a real lysimeter and found to be suitable for quantifying effective deep seepage dynamics in sandy soils. Discharge measurements and calculation results agreed well. Preconditions are accurate water content and tension measurements with high temporal resolution below the zero flux plane and an error free water balance of the calibration period. The calibration procedure has resulted in an effective unsaturated hydraulic conductivity function which allows to perform deep seepage calculations based on the measured water content dynamics only. The assumption of the unit gradient produced adequate results in sandy soils. The calculation results are exponentially sensitive to errors of water content measurements and linearly sensitive to water balance errors. However, a single incorrect water content produces only a single incorrect deep seepage value, whereas the water balance error sums up. Therefore, the quality of the water balance estimation is of crucial importance.