Let's come up with an amphibian race!

I suggest the following: For land units to submerge underwater, they need to obtain a Water Sphere (or gain the Diver skill). While underwater, they receive a penalty, but this penalty is removed with the Expert Diver skill. Amphibious units can emerge onto land after obtaining an Earth Sphere (or gaining the Land Walker skill). While on land, they receive a penalty, but this penalty is removed with the Expert Land Walker skill. All units travel across the surface sea on a ship (its chemical composition differs from the underground sea, so amphibious units cannot travel on it without a ship).