Unless we plan on equipping civilian vessels with nuclear reactors or somehow make storing gigantic hydrogen fuel cells safe the situation isn't going to change much.
"The fuel used in ships is waste oil, basically what is left over after the crude oil refining process. It is the same as asphalt and is so thick that when cold it can be walked upon . It's the cheapest and most polluting fuel available and the world's 90,000 ships chew through an astonishing 7.29 million barrels of it each day, or more than 84% of all exported oil production from Saudi Arabia, the worlds largest oil exporter." [1]
[1] http://www.gizmag.com/shipping-pollution/11526/ [2] http://www.theguardian.com/environment/2009/apr/09/shipping-...