Depends entirely on the distance and what waits on the other side. If you practice swimming a bit and eat lots of stamina foods, you can swim across most rivers and sometimes to small offshore islands. When in doubt, or if you expect danger on the other side, use the best boat you have (raft early on).

I would not advise going into the Ocean on a raft. Doing a 360 barrel roll during a storm is only fun before the monsters eat you.

Yeah, I can imagine that doesn't sound like a lot of fun. As far as ocean to lake to river, is there a way to tell the difference other than distance? Does the water change colors, etc?