An adequate characterization of river bed hydraulic conductivities (L) is crucial for a proper assessment of river-aquifer interactions. However, river bed characteristics may change over time due to dynamic morphological processes like scouring or sedimentation what can lead to erroneous model predictions when static leakage parameters are assumed. Sequential data assimilation with the ensemble Kalman filter (EnKF) allows for an update of model parameters in real-time and may thus be capable of assessing the transient behavior of L. Synthetic experiments with a three-dimensional finite element model of the Limmat aquifer in Zurich were used to assess the performance of data assimilation in capturing time-variant river bed properties. Reference runs were generated where L followed different temporal and/or spatial patterns which should mimic real-world sediment dynamics. Hydraulic head (h) data from these reference runs were then used as input data for EnKF which jointly updated h and L. Results showed that EnKF is able to capture the different spatio-temporal patterns of L in the reference runs well. However, the adaptation time was relatively long which was attributed to the fast decrease of ensemble variance. To improve the performance of EnKF also an adaptive filtering approach with covariance inflation was applied that allowed a faster and more accurate adaptation of model parameters. A sensitivity analysis indicated that even for a low amount of observations a reasonable adaptation of L towards the reference values can be achieved and that EnKF is also able to correct for a biased initial ensemble of L.