Ships float on the surface of the sea, and can be targeted by most weapons.
Hovercraft hover above the sea surface, which means that they cannot be targeted by torpedoes and depth charges.
Submarines and amphibious units move at the sea floor, can only be seen with sonar, and can only be targeted by torpedoes, depth charges, or the Commander laser.

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Water depth

Naval maps will have a combination of sea and land areas, and each unit type can move in different areas. Submarines, battleships, and flagships can only move in water with a depth of at least 17. Land units will have trouble moving in water deeper than 17.

A land unit will only be able to fire if its weapon is above the water level.

Hovercraft can move on both land and the sea surface, but cannot climb steep slopes. Amphibious units can move on land or on the sea floor at 2/3 normal speed, and can climb the same slopes as bots can. The only amphibious units that can fire while underwater are Commanders and Ducks.

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Sea economy

Shipyards and hovercraft platforms have more buildpower than land factories, and their constructors have more buildpower than land constructors do. A player focusing on sea can therefore expand their base and economy with fewer construction units, and can afford to move their commander out from their base early on. Some sea buildings are underwater, most notably metal extractors, which makes them difficult to raid.

The early energy economy for sea is based on tidal generators, which have a different output depending on the map, usually around 15. Building windmills on land can be useful to support an early sea economy if tidal strength is weak. A T1 sea constructor can build a geothermal (300E/s) if they map provides a spot near the shore. For T2 energy, uw fusions are a expensive late-game option that provides 1200E/s, but if you don't need that much power you can instead build:

an aircraft carrier has an onboard mini-fusion that produces 300 E/s

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General naval combat

Ships have a high metal cost and a low energy cost, and are larger and more expensive than land units.

Ship battles are likely to involve fewer units than land battles, and each loss has a larger impact. Ships tend to have a long range, but their slow acceleration and turn-rates make it difficult to dodge projectiles and avoid battles.

Repairing ships is very effective due to the high build power of constructors and the use of expensive units. Ships usually leave intact wreckages, as they sink to the sea floor without being hit and turned to rubble, but ship wreckages return slightly less metal than land wreckages (50% vs 66% metal).

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Sea Intel

Sea units tend to have slightly larger line of sight than land units, which helps to make up for having fewer units.
Underwater buildings and units are difficult to detect, as sonar is included on fewer units and at a lower range than normal vision.
The floating radar includes a sonar with a 900 range.
Any unit or building that has an anti-sub weapon has its own sonar with a short range, usually a bit lower than the weapon's max range.
Submarines have a medium range sonar.
Amphibious units usually have a very short range sonar.
The arm T1 ship Skater and the Cortex T1 ship Herring have a high los and their own sonar.
The T2 shipyard has an aircraft carrier that includes its own radar and sonar.
The T2 construction sub can build a advanced sonar with a high range, and the T2 ship engineer can build a advanced radar on land.
Seaplanes and T2 air have radar planes and torpedo planes that have their own sonar.

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Commander

Effective use of your commander is vital to your early strategy in sea games.

The commander walks on the sea floor making it difficult to attack, and can use its laser to fire at any units that get into range, including subs and hovers. This makes the commander effective at protecting the area around it, whether that is your early base or your frontline ships. The commander is capable of winning against a single enemy sub but will take a lot of damage doing so, and will lose against 2 enemy subs. The commander will lose by a small margin to a destroyer, but any support can help turn the duel to the commanders favor.

The commanders high build power makes it great for repairing ships, reclaiming wreckages, and building torpedo launchers and floating radar, and its ability to walk on land lets you get metal spots otherwise inaccessible by ships. If you are being overwhelmed in a team game, you can use your commander as a walking nuke to take out the enemy fleet.

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T1 Naval

Light ships

Arm has 2 light ships, the Dolphin which is specialized for close combat and the Skater which has several support roles. The decade is fast has decent health, and deals a lot of damage, but has a low los. A group of them can surround and take out larger ships or defenses. A group of Dolphins can take out an early sea base against an unprepared opponent. Early combat is likely to revolve around Dolphins while the map is mostly open before larger ships can effectively use their higher range to get an advantage. Dolphins can still be useful in mid-/late-game if you can use a large group of them to flank the opponent.

The Skater can provide vital intel with its high line of sight and short range sonar, and it has stealth (no radar signature) which makes it possible to scout the edges of the opponent's base without them seeing your unit. The Skater is equipped with a light laser, which lets it take out unprotected targets, but it loses cost for cost against other combat ships.

The Skater also has an anti-air turret, so mixing a few into your fleet can protect you from air attacks.

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Support ships

For an early attack, going with entirely Dolphins is effective if you plan on winning through force, but a mix of Dolphins and Skaters can be used for finding and taking out weak targets such as unguarded ship constructors.

Cortex has the Supporter as its light ship, which is cheaper and faster than the Dolphin, but has lower damage and health. It has a larger los than the Dolphin, but less than the Skater. Supporters are effective early on for surrounding and destroying enemy ships, but start to lose effectiveness against large fleets when stray shots and AoE (Area of Effect) can take them out.

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Frigates

The frigates for Armada and Cortex have similar stats, but the Armada frigate has 2 turrets instead of 1 larger turret on the Cortex frigate, and the arm frigate's front turret cannot fire backwards, making the unit better at attacking than defending.

Frigates have enough range and speed to skirmish well and enough health to be able to brute force through light defenses and can afford to take a few shots from a destroyer while moving into range.

Frigates can even be used against T2 ships in a brute force attack.

On a map that has a mix of land and sea, frigates can be used to skirmish with units near the shore before building destroyers.

Cortex has the Herring for its support ship, which fires tracking missile at targets with a low damage and high range, similar to the Whistler and Lasher in T1 vehicles. It has a smaller secondary anti-air turret and a high los. Adding a few to support your fleet gives you vision, anti-air (AA), and some extra ranged damage to help with battles of attrition. Herrings can also be useful for poking at enemy land units from a safe range before you can afford destroyers.

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Submarines

Armada and Cortex each have a submarine, with the Armada sub being specialized for raiding and the Cortex sub for direct combat. The Armada sub is faster and cheaper (440 metal), but has a slow fire rate, which makes it great for raiding enemy uw metal extractors. The Cortex sub is 30% more expensive (580 metal), but fires 50% faster, has more health, and a better turn rate. Two Cortex subs will trade evenly with 3 Armada subs.

Submarines can be effective at raiding since they are difficult to detect, can attack under water buildings, and most unit won't be able to intercept them. Sneaking one behind the enemy frontline and to their base can deal a lot of damage against an unprepared opponent, but subs cannot power through defenses very effectively.

The basic torpedo launcher will trade evenly with the Cortex sub. Each sub has 400 sight range and 500 weapon range, and a torpedo launcher has 400 sonar range, so it is possible to pair a sub with a support ship to kill the torp launcher from outside of its sonar range. The Armada Skater can also be useful for finding a route to send your sub to attack from.

Attacking an enemy fleet with one sub can be useful for getting incremental value and forcing them away if they have no destroyers or subs. Attacking with a group of subs can be highly effective if you can quickly take out the enemy destroyers or subs leaving the enemy fleet defenseless. If you cannot overwhelm, then added subs against a fleet with enemy destroyers will provide very little value, as destroyers can fire their depth charge and main cannon simultaneously.

On maps where land units walk through shallow water, subs can attack them without being attacked back, which can be great for taking control of a key passage.

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Destroyers

Destroyers are the largest T1 ship and have a high range (700) plasma cannon with decent Area damage, and an anti-sub depth charge turret. The Armada destroyer is slightly cheaper (880m vs 960m), slightly faster, and its turret has a faster fire rate and turn speed. The Cortex destroyer's main cannon deals more damage per shot and has a higher AoE, but its slow turret makes it weak in close combat. In long range battles of attrition, the Cortex destroyer has the advantage, but the arm destroyer's better mobility and lower cost makes it more effective early on.

If destroyers have vision they can destroy torpedo launchers from out of range, and they have a slight range advantage against floating HLTs and depth charge turrets. However, these defenses have a lot of health, and the range advantage is small enough that the destroyer has to get into position and not maneuver, making it an easy target for a counterattack. Destroyers are also highly effective against land units, as they can outrange and easily kite all the non-artillery units, and are more cost effective than T1 artillery tanks.

Resurrection Submarines

Resurrection subs can provide players a lot of value in a game, as most ships leave a whole wreck on death and resurrecting them gets back 100% of the units cost instead of the 50% that reclaiming does. Being underwater makes them difficult to target, but units that can target them destroy them quickly. Resurrection subs are much slower than the land counterpart, so it will take a longer time to revive units.

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Defenses

Torpedo Launchers and depth charge launchers are your primary options for early defense, with depth charge launchers being more effective but only buildable on land. Building one of these defenses early on can help protect your base from an early rush. Depth charge towers can help turn a shoreline or an island into a defensible position, and an elevated depth charge tower can even outrange a destroyer. Neither of these defenses can target hovercraft, so to defend against them you will need to intercept them with ships or rely on floating defenses.

Floating Heavy Laser Towers (FHLTs) have more health than the land version so that they can withstand more bombardment from heavy ships. A FHLT will trade evenly with a destroyer at half the destroyer's cost, however a destroyer can outrange FHLT.

Sea constructors are also capable of building a few land defenses. The T1 ship constructor can build a lightning/flamethrower turret and a guardian/punisher, which can be used to either get a foothold on a shoreline, or to turn an island into a defensive outpost.

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Hovercraft

Hovercraft are an expensive but versatile starting option for maps that have a mix of land and sea terrain.

The starting hovercraft platform is expensive and has a high energy cost, so its best to get at least 3 metal extractors and a group of windmills or tidal generators before building one.

A hovercraft start can get early value from an early hover constructor and from an early raid with fast attack hovercraft
Construction hovercraft are expensive, but they are fast, durable, and have a lot of buildpower, which is great for fast expansion to areas that are otherwise difficult to access
Fast attack hovercraft are only slightly slower than land scouts, but have more health and a stronger weapon. A few of these can be used to attack from unexpected angles and take out defenseless buildings, and a larger group of these can rush past and take out light defenses

Alternatively you can build a hovercraft platform later in the game as a way to switch from land or sea gameplans. This type of strategy can make good use of hover tanks, which are the main combat units used for skirmishing with other land or sea units, with enough health and damage to take out light defenses.

A midgame hover strategy can also make use of hovercraft rocket launchers, which can bombard static targets at range from unexpected angles, and attack while moving. Cortex also has access to the Halberd, a slow and short ranged hovercraft with a high health and very high DPS, closer to T2. This unit can defend your other units or be used to push through enemy units.

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T2 Naval

Cruisers

Cruisers are the base unit for a T2 fleet, with various weapons that make it good against smaller ships and hovers, a large amount of health to withstand a lot of fire, and an anti-sub weapon. Cruisers have a decent but not overwhelming matchup against every type of T1 ship, so they will win against an equal cost T1 fleet but lose against larger T1 fleet.

The Armada cruiser is faster and has a gauss cannon
The Cortex cruiser has more health and has a heavy laser

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Fast Assault Submarines

Fast assault subs are a general upgrade to T1 subs in most regards, with a higher speed, more health, and a faster fire rate with a tracking torpedo. They cost more than T1 subs, and have a lower range. These subs are effective at getting in close to take out targets, especially other subs, but will likely get into range of the enemy's anti-sub weapons while doing so. They have enough health to take some hits, but lose slightly cost for cost against cruisers and trade evenly with destroyers. These subs can also be effective at raiding due to their high speed, but it can be difficult to find an opening at the stage of the game.

The fast assault subs have a long sonar range, which lets them find and chase down uw targets such as enemy subs

The Armada Barracuda is larger and more expensive than the Cortex Predator (730m vs 950m, 1450 health vs 2100). The Piranha can win against a torpedo launcher while the shark trades with one. The Piranha can take 3 shots from a battle-sub while the Shark takes 2.

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Battle Submarines

Battle submarines have a long range (800) and deal a lot of damage with each shot, but have a very long reload time (8s). They have a decent amount of health, so it will usually take several units to kill one, which can be challenging if there are other ships or defenses that can protect it. They don't have a long sonar and they have enough los to outrange a torp launcher, but they work best when given vision with other units.

A battle-sub can destroy a T1 sub in 1 shot, a frigate in 2 shots, a destroyer in 3 shots, and a cruiser in 4 shots

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Missile ships

Missile ships specialize in bombarding land bases, with a 1550 range missile that splits apart into a cluster of bombs hitting the area around its target, which is enough to outrange most land units and defenses and all sea defenses. This unit also has a light AA with about the strength of a T1 support ship's AA, which is enough to keep a single gunship from taking it out but additional aa support is needed to fend off anything larger. Missile ships also have their own radar with 1000 range, which is enough to find targets on its own but notably less than its weapon range.

This unit is fragile, so expect it to be a priority target for enemy attacks.

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Battleships

Battleships have a longer range than cruisers (880 for Armada, 950 for Cortex), and are great at taking out anything on the surface with their high DPS cannons, but have no protection against subs or against air units.

The Armada battleship is slightly faster and has 2 main cannons and is better at long-range bombardment and at kiting
The Cortex battleship has 1 heavier main cannon, a heavy laser, and more health. The extra durability and laser makes it more difficult to take out at close range

Cruisers can win against a battleship if they get in close and surround it, so its not a good idea to send a battleship on its own without support if you can't take advantage of its range.

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Flagships

Flagships are the largest sea unit, and have a variety of weapons

The Armada Epoch has 2 main cannons for bombarding targets at 2450 range, and the Cortex Black Hydra has 1 larger set of cannons.

The Epoch has smaller cannons for closer-range battles that can all fire at once when the ship is facing forward, and the black hydra has heavy lasers that can all fire at once when the ship is facing to the side. The Epoch is slightly faster and cheaper, and the black hydra has slightly more health.

Both flagships have their own radar and have light aa to fend off small groups of air units, but need extra support to stop a large air attack. Flagships have no anti-sub weapons, so bring some T2 subs or cruisers along to protect them. When bombarding land targets at range, the black hydra has enough firepower to break through one plasma deflector, and the epoch can barely break through two.

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Carriers

Carriers act as general support ships for a T2 fleet, providing an anti-nuke, a portable fusion producing 300E/s, a long range radar, a mid range sonar, a large los, and a pair of air repair pads. It is almost always worth building one of these late game to support your fleet and base.

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Constructors

T2 sea has 2 constructors, the construction sub which focuses on T2 econ buildings and the naval engineer which can build a variety of T1 ships, a few T1 buildings, naval mines, and a few land buildings including a T1 metal extractor, an advanced radar, and various naval defenses. Both constructors can build all of the T2 defenses. The naval engineer is cheap, making it very effective at assisting other builders and useful for reclaiming and repairing. The Armada naval engineer can build Platypus, which allow for a land invasion without having to build a amphibious or hover factory.

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Defenses

For T2 sea defenses, bot factions have an advanced torpedo launcher and a heavy floating defense, Kraken for Armada and Devastator for Cortex. While both defenses have similar costs, the advanced torpedo launcher has a lower health and DPS, but its long range tracking torpedo is very effective against subs.

The Kraken and Devastator are effective against surface ships, especially T1 fleets and cruisers.

Rushing out one of these defenses after getting to T2 can help you survive while you build up a T2 fleet. These can also be an effective but expensive option to defend against a large hover attack.

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Amphibious Units

The T2 bot lab for Armada has the Platypus, which swims on the sea surface and acts like a hovercraft, and has a similar cost effectiveness as normal hovercraft. These can be useful for a surprise invasion from a coastline or an attack on an enemy sea base.

The T2 bot lab for Cortex has the Duck, which move as an amphibious unit but has an underwater torpedo launcher. It has more health than subs, which makes them difficult to kill, but they have a long reload time which limits the amount of damage they will deal. These can be effective in small amounts to raid an sea player, as they are difficult to detect and can take out uw metal extractors. A player with an overwhelming economy can build a large group of these to completely remove a weaker sea player from the game.

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Seaplanes

The seaplane lab has access to a torpedo gunship, and the T2 air lab has access to a torpedo bomber.

These are both effective ways to take out underwater units and buildings without having to rely on ships, and they can also act as a counter to subs.

Seaplanes are generally stronger than T1 Aircraft, and can be a very powerful surprise.

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T3 Units

Each faction's T3 gantry has access to a T3 hovercraft, which is similar in strength and cost to a T2 heavy tank, and is an effective late game option for fighting against a strong sea player.