<p>The sizing of the main span dimensions for new marine bridge crossings needs to consider the current shipping vessels using the waterways and the future growth in marine traffic. Internationally accepted guidelines are used for initial sizing of the navigation clearances, but confirmation of the safe passage of vessels requires simulations to be undertaken. For two major marine bridges planned in the Philippines the marine navigation clearance assessments have been carried out, and the results verified via realistic simulations carried out at the facilities available in the Maritime Academy of Asia and the Pacific (MAAP). This paper outlines methodology of the theoretical calculations and the simulations performed, which confirmed the clearances and informed the design of the required navigation aids.</p>