A new method of integrating satellite remote sensing data and inundation models allows the mapping of extensive tidal mudflats in a sub-Arctic estuary, Cook Inlet (CI), Alaska. The rapid movement of the shorelines in CI due to the large tides (~10 m range) is detected from a series of Landsat imagery taken at different tidal stages, whereas GIS tools are used to identify the water coverage in each satellite image and to extract the coordinates of the shoreline. Then, water level along the shoreline for each satellite image is calculated from the observed water level at Anchorage and the statistics of an inundation model. Several applications of the analysis are demonstrated: 1. studying the dynamics of a tidal bore and the flood/ebb processes, 2. identifying climatic changes in mudflats morphology, and 3. mapping previously unobserved mudflat topographies in order to improve inundation models. The method can be used in other regions to evaluate models and improve predictions of catastrophic floods such as those associated with hurricane storm surges and tsunamis.