Christian (above) is right. Currently your question is very broad and difficult to answer. You might want to do some research yourself and then ask a more targeted question.
Start looking at shallow water equations for example. (I'm skipping full fluid simulations here for the moment) Or read Tessendorf's "Simulating Ocean Waves". Or have a look at Cem Yuksel's wave particles. Even if you don't end up implementing any of it, the references will be a good resource for you. Another one might be this collection of links.
Not really a clear answer, but give us more to go on and we can point you in a more specific direction.
