From StrategyWiki, the free strategy guide and walkthrough wiki

Fighting on water is very different than fighting on land. For one thing, there is usually less space to maneuver and the units are much more limited. The downside to naval units is that they are not amphibious, and once you have conquered the seas you will have little opposition in those areas of the maps. However, if there are any resources along the coast, your naval units can help defend them.