Summary An attempt was made to improve the application of a lumped parameter model in the unsaturated soils planted with different crops. A first step of such an improvement was shown in Stumpp et al. [Stumpp, C., Maloszewski, P., Stichler, W., Fank, J., 2009. Application of the environmental isotope δ18O to study the water flow in unsaturated soils planted with different crops: 1. Case study – Lysimeter station “Wagna”, Austria. Journal of Hydrology] where the tracer concentrations in the recharging water were weighted according to the precipitation rate and by separating the observation period to different vegetation sub periods. However, during strongly variable flow conditions this improvement was still not sufficient enough to yield adequate modelling results. Therefore, in the present paper we investigated the flow processes in a high sophisticated lysimeter setup. The lysimeter had a length of 2 m and a surface area of 1 m2 and was weighable which yielded water content as a function of time. This data enabled a further development of the lumped parameter approach to variable flow conditions. A new method was found to estimate the tracer concentration in the recharging water (input function) that takes the actual evapotranspiration rates into account which was indirectly determined from weighing the lysimeters’ mass. Thus, it was possible to use a lumped dispersion model with such a new estimated input function to investigate the δ18O transport in soils planted with crop rotation with relatively high accuracy. The results obtained with the lumped dispersion model were compared with more exact numerical transient flow modelling, which however requires more detailed soil hydraulic data. The results of both modelling approaches yielded similar system parameters. The lumped parameter approach resulted in water contents of 0.14–0.30 cm3 cm−3 during the different vegetation periods and a mean value of 0.22 cm3 cm−3 for the whole observation period. The transient flow modelling yielded a mean water content of 0.21 cm3 cm−3. The dispersion parameter found in both models was in the same range. This study shows that a lumped dispersion model is applicable in the unsaturated zone even under strongly variable flow conditions having additional information about the water balance.