In the framework of the Danube Environmental Program a study on the Nutrient Balances for the Danube Countries has been completed. The method of materials accounting was applied to calculate nutrient flows (including emissions into surface waters) which is based on mass balances among different components of the anthroposphere and its environment. The evaluation indicated the significant role of uncertainties and errors of various sources which are determined primarily by methodological and data related reasons. Thus, even if the entire system is numerically balanced, the procedure can lead to incorrect results (which remain hidden). To demonstrate the role of uncertainties, one component of the system, the agricultural sector was chosen. Eight major input and output nutrient flows were involved (such as agricultural nutrient discharges into surface and groundwater, and tropospheric losses). These flows (which are not independent of each other) can be estimated from linear and non linear functions of statistical data and a large number of parameters in a wide uncertainty range. To perform an error analysis, traditional (sensitivity analysis) and Monte Carlo simulations were combined. The relative contribution of the errors of parameters was analyzed. Conclusions were drawn on the applicability of the materials accounting for the estimation of agricultural N and P emissions into surface waters and cross-checking of the different propagation ways become possible.