You can make naval units without changing any of the units on land.
I once made (not finished though) a strategy map where every race had 3 ships (no shit, the models were already in the game)
Ships are built very slow but have a huge amount of health.
They had a transport ship. The transport ship has very low health and cannot attack.
The transport ship was only good to get units past the walls of the enemy (yea I had walls too)
The units can only be dropped in small areas because most of the sea is deep water.
They had a frigate. The frigate is a ship that is specialized at destroying other ships (transport ships and battleships)
If the enemy has no ships, dont create frigates.
The frigate is the basic war ship. All other warships are compared to the frigate.
They had a battleship. The battleships are slow moving, low dps, high ranged units... like catapults.
They deal very much AoE damage but have a very low fire rate.
Because of their range they can destroy buildings that are not too far away from the water.
With those three ships you have pretty much what you want.
You have a reason why to build ships and you have something to fight them off.
The thing is that there is actually only one warship (assuming that people wont use massive armies so a battleship will actually help in naval battles too)
You might want to have another ship that is specialized in destroying other ships but cannot attack air and make the frigate have lower damage for example.
Or a ship that has some builders on board so it can repair ships at sea.
Maybe a demolition ship? (One that explodes to deal damage.)
Just use your imagination
EDIT: Ofcourse this will be going a bit back from the WC3 basics where everything is playing alongside heroes.
This is more of a thing for a bit bigger rts games.