River restoration measures are becoming increasingly popular and are leading to dynamic river bed morphologies that in turn result in complex water level distributions in a river. Disconnected river branches, nonlinear longitudinal water level profiles and morphologically induced lateral water level gradients can evolve rapidly. The modeling of such river-groundwater systems is of high practical relevance in order to assess the impact of restoration measures on the exchange flux between a river and groundwater or on the residence times between a river and a pumping well. However, the model input includes a proper definition of the river boundary condition, which requires a detailed spatial and temporal river water level distribution. In this study, we present two new methods to estimate river water level distributions that are based directly on measured data. Comparing generated time series of water levels with those obtained by a hydraulic model as a reference, the new methods proved to offer an accurate and faster alternative with a simpler implementation.