Unfortunately RTW don't feature naval battles. Answer quoted from the FAQ :

"Q. How important is Naval units in RTW. How do you get your men across the Mediterranean Sea, with out walking.

A: Naval combat is abstract in Rome: Total War. The emphasis in the game is on land battles - the Romans were, after all, soldiers rather than sailors - and we've been working hard to make them as insanely great as possible. Unlike M:TW fleets now carry passengers from place to place. An army has to march onto a fleet, be carried to its destination, and then disembark. While the army is aboard it can be lost through enemy action and natural disaster, and a storm can wipe out an invasion force just as surely as enemy triremes!"