Abstract. Marine-based sectors of the Antarctic Ice Sheet are increasingly contributing to sea level rise. The basal conditions exert an important control on the ice dynamics and can be propitious to instabilities in the grounding line position. Because the force balance is non-inertial, most ice flow models are now equipped with time-independent inverse methods to constrain the basal conditions from observed surface velocities. However, transient simulations starting from this initial state usually suffer from inconsistencies and are not able to reproduce observed trends. Here, using a synthetic flow line experiment, we assess the performance of an ensemble Kalman filter for the assimilation of transient observations of surface elevation and velocities in a marine ice sheet model. The model solves the shallow shelf equation for the force balance and the continuity equation for ice thickness evolution. The position of the grounding line is determined by the floatation criterion. The filter analysis estimates both the state of the model, represented by the surface elevation, and the basal conditions, with the simultaneous inversion of the basal friction and topography. The idealised experiment reproduces a marine ice sheet that is in the early stage of an unstable retreat. Using observation frequencies and uncertainties consistent with current observing systems, we find that the filter allows the accurate recovery of both the basal friction and topography after few assimilation cycles with relatively small ensemble sizes. In addition it is found that assimilating the surface observations has a positive impact on constraining the evolution of the grounding line during the assimilation window. Using the initialised state to perform century-scale forecast simulations, we show that grounding line retreat rates are in agreement with the reference; however remaining uncertainties in the basal conditions may lead to significant delays in the initiation of the unstable retreat. These results are encouraging for the application to real glacial systems.