Let’s start with Terran:
Terran ships would be built out of a new building called the ship yard. It would be a tier two building roughly analogous to the starport
The first unit is the Poseidon class battleship. This is the equivalent of the thor or battlecruiser, it does a lot of damage and has a lot of health. It a has a researchable ability called “Broadside” that does similar types of damage as the 250mm strike cannons.
The next unit is the Marlin. It is a medium versatile combat ship capable of targeting both sea and air targets simultaneously. It doesn’t have a strong attack but it has really fast dps. It also has a researchable ability called sonar allowing it to detect all submerged (aka cloaked) vessels in the area for a short period of time.
The final terran unit is the Boomer (if you’ve played Yuri’s revenge please get over the name). It is permanently submerged and has six missiles that must be built in order to fire (a la interceptors). This ability can be autocast and does a large aoe. However this unit is extremely weak, one marlin and it’s toast. It can be upgraded to carry eight missiles.
The Protoss warp in sea units at the hydrosphere, it’s available to build once the cyber core is built.
The first Protoss unit is the purifier. This is a powerful surface warship designed to cleanse the sea. It has a medium strength attack and lots of shields. It also has a researchable ability called electrosalinization which does a large amount of aoe and does bonus to biological units (think psi storm).
The next Protoss unit is the Trident. This is the bread and butter Protoss sea unit, good attack good shields and defense and good shields. It is a ranged attacker which shoots twice dealing one half of its damage per shot but the shots cannot be dodged. Though unremarkable, this unit is essential for the Protoss to establish control of the sea (think a cross between an immortal and a stalker).
The final protoss unit is the Atlantean. It serves a protector role, it has a very weak attack and low shields and health but when it submerges it becomes a detector. It can remain submerged indefinitely but cannot attack while submerged.
The Zerg morph sea units from a seed pool, this is a lair level building. All zerg swimmers have the ability to submerge for a short period of time once it has been researched. Zerg swimmers can also move while submerged
The first Zerg unit is the krakelisk (please give me a break on the unoriginal names). This many armed Zerg melee swimmer lashes enemy vessel until they sink. Not much to say here, it has the health of an ultrlisk.
The next zerg unit is the kniferay. A sneaky swimmer, it has an electric shock attack that ignores shields and can attack when submerged. It has a researchable ability that allows it to charge up a power shot that is extremely strong and does a small aoe. However when doing this the kniferay takes thirty percent more damage.
The last zerg unit is the piranha. Cheap and easy to kill it nonetheless packs a punch, this melee unit has a researchable ability called feeding frenzy that increases it’s attack speed by five percent for every piranha within a certain radius.
There would be special island maps with water where these units would be viable. The zerg overlord would be able to morph into an aquatic version of an overseer; the overseer could spawn creep to contaminate the water slowing enemy ships down. The Raven, observer, scan and overseer can all see submerged units. Colossi can walk through water however they half their movement speed when doing so. All ships with range can attack land as long as it is within their los, same goes for land units.
I’m actually having a lot of fun writing this but it’s getting late so I’m going to post this and come back in the morning. If anyone has any suggestion I’d love to hear them (especially regarding Zerg unit names )