Ewoks don't look like they'd fare too well underwater to me, they look like they'd just get soggy and drown (YES!). They'd find it kind of hard to get those gungan jellyfish towns.

Either way it'd be a very boring war with probably very few casualties since neither side seems capable of developing stabbing weapons (although one has mastered flight and the other has mastered sheild technology - but still depends on giant beasts of burden to convey it).