In Europa Universalis II, when you have military access in a country you can sail fleets into that country's ports. This is true even if you are currently at war. You can also, of course, sail your fleets into your own ports. If a fleet ends its move in an enemy port settlement, and the settlement is unfortified, the settlement is captured. It is captured regardless of whether it is occupied by land units; land and sea units do not interact, so there is no battle.