Water and element fluxes in the unsaturated zone of soils are most often calculated on the basis of average water fluxes and average soil solution concentrations. However, if the input of water and elements exhibit a strong systematic variability, this will most likely be reflected in the flow of water and elements in the soil. In such cases the ‘average’ based calculations will be subjected to significant errors. In order to overcome this problem, the present paper describes a method to calculate the water and element fluxes in the soil of a Norway spruce plantation taking into account the known stem-distance related variability in both water and element fluxes. The calculations are based on studies and previous findings of spatial variability in a Norway spruce plantation in Denmark. The suggested method leads to an improved Cl-balance when calculated for 6 years. The possible factors responsible for the errors in water and element fluxes are discussed and preferential flow paths, sampling under big trees, errors in modelling evapotranspiration and incorrect weighing between subareas are concluded to be most important.