NavTEL is a new decision support tool for the short-term (36 h) planning of ship routes and the management of underkeel clearance in estuarine navigation channels. NavTEL uses a deterministic method and is coupled with the TELEMAC-MASCARET system for numerical modeling of hydrodynamic and sediment transport in the estuary with a two-dimensional approach. In its present version, NavTEL allows (i) daily simulations to be automatically prepared and launched; and (ii) simulation outputs to be postprocessed to find the safest ship route and to predict underkeel clearances at specified locations. As the reliability of the results relies on the accuracy of water-level predictions, numerical simulations were performed with measured river discharges, storm surge forecasts, and time-varying friction coefficients for bed roughness. Even though NavTEL was initially developed for the Atlantic Port of Bordeaux located in the Gironde Estuary, its kernel has a modular structure allowing the tool to be adjusted to different port configurations and types of water bodies. Finally, examples of graphical outputs and reports generated by NavTEL are shown for an application of a container ship coming into the port of Bordeaux.