We consider the problem of conditioning a geological process-based computer simulation, which produces basin models by simulating transport and deposition of sediments, to data. Emphasising uncertainty quantification, we frame this as a Bayesian inverse problem, and propose to characterize the posterior probability distribution of the geological quantities of interest by using a variant of the ensemble Kalman filter, an estimation method which linearly and sequentially conditions realisations of the system state to data.A test case involving synthetic data is used to assess the performance of the proposed estimation method, and to compare it with similar approaches. We further apply the method to a more realistic test case, involving real well data from the Colville foreland basin, North Slope, Alaska.