In urban drainage the estimation of runoff with the help of models is a complex task. This is in part due to the fact that rainfall, the most important input to urban drainage modelling, is highly uncertain. Added to the uncertainty of rainfall is the complexity of performing accurate flow measurements. In terms of deterministic modelling techniques these are needed for calibration and evaluation of the applied model. Therefore, the uncertainties of rainfall and flow measurements have a severe impact on the model parameters and results. To overcome these problems a new methodology has been developed which is based on simple rain plane and runoff models that are incorporated into a stochastic state space model approach. The state estimation is done by using the extended Kalman filter in combination with a maximum likelihood criterion and an off-line optimization routine. This paper presents the results of this new methodology with respect to the combined consideration of uncertainties in distributed rainfall derived from radar data and uncertainties in measured flows in an urban catchment within the Emscher river basin, Germany.