A possible solution may be found by reading The Gateway Special by Jerry Oltion. The author proposed the use of a submarine and providing it survives the transition into space it should also be capable or returning to the environment that it was designed for. It is not an elegant solution but it is at least a solution.

Pressure

Short answer: Spaceships aren't designed to be under pressure.

Long answer: Most spaceships operate in space. There is generally none (or negligibly little) air in space, and, assuming the spaceship is carrying humans, there will only be one atmosphere (~14 PSI) of pressure inside of the spaceship. On the other hand, water is much, much denser than air, so most submarine ships (like submarines) are built to endure high pressures. The pressure at 490 meters (the operating depth for the Seawolf class nuclear submarine) is roughly 1672 PSI. A spaceship would simply be unable to withstand such pressures.

Propulsion

Short answer: Rockets are not entirely waterproof, and rocket engines don't as well underwater.

Long answer: Liquid-propellant and solid fuel rocket engines both contain oxidizer as well as fuel, so in theory they would be able to operate underwater. Unfortunately, one of the main issues with this is that ignition would be impossible underwater. Additionally, many spaceships are not entirely airtight; only the passenger-bearing sections are airtight. This creates issues, as water could leak into the spaceship's cavities, and water does not play well with electronics (and many other things).

Maneuverability

Short answer: Spaceships are not adapted to water resistance.

Long answer: As we mentioned before, water is very dense. Spaceships generally operate in a vacuum, so water/air resistance is not a problem for them. Unfortunately, water is much more constrictive than air/vacuum conditions, so streamlining your spaceship becomes essential when it goes underwater. Otherwise, fuel will be wasted, as the craft is not hydrodynamically optimized.

Corrosion

Short answer: Water will corrode your spaceship.

Long answer: Spaceships are not in contact with corrosive compounds (generally), except possibly the engine (which is constantly in contact with oxidizers). Sea water is highly corrosive (it is very saline, and salt does not play well with metal), so a spaceship that regularly (or even occasionally) went underwater would require oxidization control (in addition to all the other modifications they would require to go underwater). Many ships, vehicles whose only job is to be underwater, don't have this down, which means that corrosion-proofing a spaceship will prove to be incredibly arduous.

Conclusion

Spaceships cannot go underwater because they are not designed to withstand pressure, are not built to withstand water leakage, will corrode due to seawater, and are not optimized to travel through water.

The pressure of the water is sure to damage the ship because it was not designed to submerge. Another problem would pose the propelling system. Depending on what type of propulsion the ship uses, many do not work if suddenly torrents of water are flooding the engine room or the reactor or whatever is there.

The Star Trek universe contains a number of examples of spacecraft operating in either liquid or high-pressure gaseous environments, including:

• The Delta Flyer (Voyager episodes "Extreme Risk", "Thirty Days")
• USS Voyager (episode "Scorpion")
• USS Enterprise (TOS: The Immunity Syndrome)

In each case, the "realities" of the situations are either ignored or handwaved. The Delta Flyer is supposedly built from special (ambiguously specified) materials to enable it to operate in the atmosphere of a gas giant, but it is somehow also able to, in a later episode, comfortably splash down into and operate submerged in an aquatic environment for which it wasn't originally designed. Similarly, Voyager somehow enters, and successfully navigates "fluidic space", and the Enterprise (and one of its shuttlecraft) successfully enters and navigates the protoplasm of a giant (planet-sized) cell.

The point here is that these are examples of more fantasy sci-fi than hard (science-based) science fiction. Although the Star Trek franchise draws on science advisors, it seems to be more for convincing techno-babble than scientifically plausible scenarios.

In posing the question "Why can't they..." you need to consider examples where is does occur, and how (if at all) it is explained in-universe. As stated in other answers, spacefaring and submersible structures have very different, if not contradictory, design requirements. Sure, you could probably launch a submarine into space, and it might successfully contain an internal atmosphere, but it would be awfully (impractically) heavy for something that needs to be accelerated to very high velocities to get anywhere worthwhile in a reasonable amount of time.

There are many problems.

1. The water itself:

Spaceships are designed to travel in near-vacuum environments. Thus, aerodynamic design doesn't really matter. Even if the spaceship decides to enter the atmosphere, it can probably shoulder its way through. But water? Water is DENSE. Submarines need some serious aerodynamic design to cut their way through water efficiently. If a spaceship is not designed aerodynamically, trying to travel through water would be like swimming through gelatin: slow and seriously not fun.

2. The pressure:

Spaceships are designed to travel through space. In case this was not common knowledge, space is REALLY empty. The hull of a spaceship is more concerned with keeping stuff that's inside, inside. As something goes deeper into the water, the pressure increases. There is a reason submarines are built with thicker armor than tanks. If a spaceship tries to go deep, it will quickly develop leaks and may even crumple like a tin can.

3. The entry:

You have all heard the saying: Falling from high up, water and concrete are about the same. Thus, things entering water must either start from inside it or present a small surface of impact. Considering that spaceships are gigantic, flat, fuel-guzzling super-fast monstrosities, they would probably break apart on impact with the water.

4. The reasons:

There's a reason why spaceships are called SPACE-ships. They are optimized for space travel, and space travel only. It is much better to have specialized vehicles for every job than a jack-of-all-trades-master-of-none. There is no reason someone would take a spaceship into a water body, when they could just as easily get a submarine down from the ship and do the same job with much more ease and convenience.

of course it depends on the universe, or rather the spaceships in the universe, but a likely explanation is pressure. In space there is hard vacuum. under water there is heavy external pressure. Even if the engines would work (pretty big if), the hull wouldn't survive the pressure for long.

Short Answer

In a realistic world, most vessels will be optimized for a single environment (space for space stations, bicycles for land, or submarines for underwater). Some vessels may be capable of travelling in two environments, but they aren't good at either environment, and the more different the two environments are, the harder it is to justify the vessel's existence in your world.

For example, although flying cars exist...sort of (see image below)...they are not commercially viable. They’re too expensive for the daily commute to work (bikes, busses and cars are the better alternatives), but not efficient enough for cross-continental flights (a commercial jet would be better).

That's not to say a vessel that could travel in sea and space couldn't exist...but there would have to be a compelling reason for it to exist. For example, an ocean planet specializing in underwater mining and trades with other star systems may have reason for space ships to double as submersibles --- but even in this extreme case, those needing to be underwater (the miners) would not be the ones needing to be in space (the traders).

Such a vessel might exist as a toy for a very wealthy person, or a spy-fi gadget (like James Bond's submersible car--see below), or as an experimental craft in a research lab. There's almost certainly no reason for it to exist in common use because it would not be commercially viable.

You asked for thoroughness....

Qualification: I'm a graduate-level planetary scientist specializing in fluid/atmospheric dynamics and a lover of science fiction.

A more thorough answer depends on lots of things, but in terms of physics, it comes down to density, speed of travel, pressure, and technology.

Density and Speed of Travel

The denser a medium is, the more effort it takes to move through it. This is why it's easy to move through air, harder to move through water, and difficult to move through a thick mud (there are other effects at work, but density alone would be sufficient to explain those observations).

The faster you move through a fluid, the more it resists your motion.

In fluid dynamics, these effects are captured together in the concept referred to as "ram pressure". This "pressure" is the slowing force per unit area that an object moving through a fluid experiences and is generally proportional to the speed of motion relative to the fluid times the density of the fluid. Ram pressure is the force per unit area that an object experiences as it pushes away particles in a fluid it is moving through. To an expert, "ram pressure" is slightly different than "air resistance", but it's similar enough that you can probably think of them as the same in many situations.

When gravity causes a skydiver to fall faster and faster through the atmosphere, the atmosphere's ram pressure on the skydiver increases with speed (and very slightly as the atmospheric density increases closer to the surface). When the ram pressure times the cross-sectional area of the skydiver equals the force of gravity, the forces balance and the skydiver reaches terminal velocity.

Pressure

As others have noted, spaceships are built to withstand certain pressure conditions. They must withstand explosion (from internal air pressure) in the vacuum of space and equalized air pressure on the surface of a planet.

The surface pressure at a given point on the surface is literally equal to the weight per unit area of the atmosphere above it. The same is true underwater: the pressure at a given depth is equal to the surface pressure (one atmosphere) plus the weight of the water per unit area above that depth.

Here's where things get fuzzy: Some planets, like Jupiter and Saturn, have very thick atmospheres. On one hand, a given world might have a really thick atmosphere -- in which case spaceships visiting the planet would be need to be built more like submarines to withstand the incredible pressure. On the other hand, the atmosphere might be thin, and the "ocean" might be of some exotic liquid that is less dense than water. In that case, submarines wouldn't need to be as heavily fortified against pressures because the pressure would increase with depth less than it does in Earth's oceans. In either of these two cases, submarines might look more like spaceships, depending on the depth they are designed for.

As others have noted, a thicker shell to protect a vessel from pressure extremes is heavier. The added mass would mean that propulsion systems would have to work harder. Thus a heavier ship would require bigger (or better) engines and/or more fuel -- both of which would add to the mass of the ship, which would require more fuel, and so on. For more information, read about the rocket equation.

Propulsion

• Jet engines would not work because they take in air (oxygen). They would not work well in the vacuum of space and would not ignite.
• Rockets work fine underwater in theory because they require no air (up to a limiting pressure) -- this is why they work well in space.
  • Extremely high pressures would push the outside fluid into the rocket, totally overwhelming the rocket so that it could not force exhaust out the nozzle.
• Propellers work well underwater, but not in space because they work by pushing material backwards, which causes the ship to move forward. There's essentially nothing to push in space.

As far as futuristic and/or hypothetical propulsion systems, it depends on the technology, the density, and on the universe. Can faster-than-light engines work underwater? Ask the author/owner of the universe why or why not.

Transition Between Atmosphere and Ocean

A spaceship needs to be capable of entering an atmosphere smoothly from the vacuum of space. For this reason, many have struts to slow them down as they enter the atmosphere at tremendous speed and heat shields to dissipate the heat. This works because the density varies very slowly between the top of the atmosphere and the surface. Physically speaking, the slowly-increasing density means the ram pressure on the vessel varies slowly enough so that the ship -- and its occupants! -- do not experience a sudden and damaging deceleration.

Any vessel that travels from an atmosphere to an ocean will need to be built for the transition from the lower-density atmosphere to the higher-density ocean. Human bodies can handle the transition at low speeds, like when we jump into pool water from the side, but not at higher speeds, like when we belly flop from a high diving board 10+ meters above the surface of a body of water.

High Speed Impact: more potential for damage

Low Speed Impact: less potential for damage

This is because the higher speed increases the ram pressure. The ram pressure of the air is negligible, but the ram pressure as we hit the water can be painful! In exactly the same way, and for exactly the same reasons, any vessel transitioning between atmosphere and ocean would need to be built to withstand the sudden -- and potentially dangerous! -- increase in ram pressure that would slow the vessel down. The ram pressure is minimized when the surface area is decreased. This is why belly flopping (larger surface area ==> larger ram force ==> larger deceleration) hurts more than diving in with arms crossed at the chest and toes pointed down (smaller surface area ==> smaller ram force ==> smaller deceleration).

High surface area dive: more potential for damage

Low surface-area dive: less potential for damage

On Earth, a spaceship travelling more than a few dozen meters per second would break apart on impact if it tried to "dive" into the water, unless it were significantly more fortified than our current technology allows.

This effect would be more pronounced for planets with low-density atmospheres and high-density oceans, and it would be less pronounced for planets which have a smaller difference in density between the atmosphere and ocean.

Shape Considerations

Because the density in an ocean is very high, the ram pressure is significant. For this reason, our submarines have a streamlined shape to minimize the ram pressure and the drag.

Assume for the sake of argument-by-intuition that the International Space Station had engines and a strong enough hull to move around underwater. It is not in an efficient hydrodynamic shape and the engines would have to work very hard. Moreover, if travelling fast enough through the water, it's possible some of its components would break off.

Spaceships meant only for space do not need to have aerodynamic or hydrodynamic shapes because they do not travel through air or water. Example: the Death Star or orbital space stations.

Spaceships which land on planets need to be at least somewhat aerodynamic so that they do not burn up in the atmosphere or have parts break off. Example: X-wings in Star Wars or the USS Enterprise starship from Star Trek. The faster the atmospheric entry speed, or the greater the density gradient in the atmosphere (e.g. the greater the planetary gravity), the more pronounced this effect will be.

Some vessels, such as the TARDIS from the Doctor Who universe, can land on a planet without travelling through atmosphere or ocean. For this reason, they don't need to be aerodynamic or hydrodynamic.

Summary / Conclusion

Different vessels are built for different purposes. If a ship is built for a particular set of conditions (e.g. space-only, air-only, underwater-only), it can be optimized for those conditions. If a vessel is designed to experience very different sets of conditions, it is much more difficult to optimize the ship to both sets of conditions, so sacrifices (e.g. sub-ideal designs like higher mass ships) must be made. The more different these conditions are, the harder it is.

In theory, a car can be made into a submarine, but it would be neither a great submarine nor a great car:

A vessel can go in the air and on the ground, but it's neither a great car nor a great plane:

A plane can go into space, but it is neither a great plane nor a great spaceship:

These outlandish transport vessels attempt to make travel possible in just TWO different environments with a single transition. For a spaceship to travel underwater, it would need to be designed for water, air and space — THREE different environments with two transition regions.

You're missing the middle layer of air between the vacuum of space and liquid water.

You can have spaceships that never enter atmosphere thus have different propulsion and shape to aircraft that never leave atmosphere which in turn has a different propulsion and shape to a submarine.

Each vehicle type has different problems and completely different engineering. Spaceships need radiation shielding. Submarines need water proofing. Aircraft needs aerodynamic design.

In theory you could make a spaceship that can go underwater but it makes it more expensive and complicated than having three separate vehicles and less efficient than a specialist vehicle.

If your unable to close the "open" nozzle at the end of your spaceship couldn't you just say that if the seawater entered into the ship through the nozzel any left behind traces of seawater would cause engine failure or cause the engine to blow up? thus eliminating the ability of the ship to go underwater. or that the ships hull is made of a special alloy that has a reaction to seawater that causes a deficiency in hull integrity making space travel no longer viable for said ship.

It's also a matter of efficiency. Spacecraft are weight sensitive: the more mass, the more energy needed to move the spacecraft. This is especially prevalent when moving from the surface of a planet to orbit, where the spacecraft has to counteract the planet's gravity.

One could build a spacecraft that could also travel underwater. The streamlining to reduce atmosphere friction when going from surface to orbit would also add benefits while underwater. Since both situations require an artificially created atmosphere, the life support system would be essentially the same... both submarines and spacecraft today have systems to remove CO2 from the air, and add oxygen.

However... the pressures involved underwater are the opposite of what a spacecraft encounters... instead of 1atm pressing from the inside outward, a submarine deals with pressure from the outside pressing inward. Also, the pressures involved underwater are far greater, requiring a much stronger (and heavier) construction that would be of no benefit while in space.

So, while you could build a spacecraft that can also go underwater, it would be extremely heavy, requiring huge amounts of energy to move.

A more efficient approach might mirror the LOR method used for the Apollo moon missions: a main spacecraft built for long distance travel and re-entry, with a specialized spacecraft optimized for the moon landing. Your spacecraft could just carry a small submarine for underwater operations, without paying the huge weight penalty of taking the entire spacecraft underwater.

To directly answer the question, the reason a ship in a science fiction story can't go under water is because it's a plot device meant to further some part of the story. At that level there's no reason for it beyond what the author decides.

If you're looking for a more "reality" based answer, the answers about the design differences between submarines and spaceships were pretty good. Another thing to consider is that a "real" spaceship probably wouldn't be able to enter an atmosphere without burning up. A "real" spaceship would likely be unable to do anything but slightly alter where ends up crashing if it tried to land on a planet. And any ship that actually made it to the surface in one piece, would be unlikely to ever escape the planetary gravity well afterwards. You really need to be able to do all of these before you can even consider going under water.

I'm going to challenge this.

All spaceships capable of landing are able to do this.

The Space Shuttle glided to its landing. Not very well, admittedly, but it's another case of Samuel Johnson's performing dog - you're amazed to see it happen at all. SpaceX have put a substantial amount of effort into landing a rocket on its tail. But the Mercury, Gemini and Apollo capsules all splashed down into the ocean. Clearly therefore they can survive at least some immersion in water. It's not known exactly how far they sank after splashdown before they floated to the surface again, but they will have gone properly under.

These American capsules were all designed to float. The Soyuz is not, and their missions have all intended to land on the steppe, so no-one needed to make sure they floated. Except that Soyuz-23 landed on a frozen lake, crashed through the ice and sank to the bottom. Lake Tengiz is apparently between 2.5m and 6.7m deep. The capsule (and cosmonauts) survived perfectly well - the only problem was waiting to be retrieved.

Why are capsules able to do this, when the walls of the ISS are so flimsy? The simple answer is that they're built for re-entry. When you think that the capsule is designed to expose its crew to no worse than continuous 10G loads, that needs some serious structural strength! Whilst most of this load will apply vertically on the capsule, there are substantial side loads too, so the capsule needs to withstand very large stresses in all directions.

This translates to pressure on panels as well. In space, there is naturally 1atm of pressure from the inside out. On re-entry though, there is an engineering challenge to keep superheated air out of the structure - this is what caused the loss of Columbia. So all panels must withstand some significant pressure from the outside as well. The ISS can make assumptions about panels pushing outwards, but anything going through re-entry has to have panels locked in both directions. I don't have a figure for this, but I'd expect at least a couple of atmospheres of pressure.

This gives us a definitive answer. If your spaceship cannot enter the atmosphere, it probably cannot survive underwater. But if your spaceship is built to enter the atmosphere, then it will always be able to survive underwater to at least some degree. Exactly how deep would need more detailed knowledge of the specs your hypothetical spaceship was built to, but no-one should be surprised at it being perfectly happy underwater. If it's rated for 2 atmospheres of external pressure during re-entry, that means it's rated to 10m depth.

The other answers already provided the biggest issues such as the spacecraft being designed to have higher pressure on the inside than the outside, fortifying it even more to get deeper than a few metres would increase mass and therefore fuel consumption... The same applies to ballast needed and another way of propulsion. All of this would make it hard or even impossible to reach high speeds and transport a lot.

Another thing not mentioned are that materials used in spacecrafts today will be damaged by saltwater or whatever the ocean/lake will be made of.

One possible craft I could think of were something similar to a spaceshuttle that can be used like a seaplane by shielding the engines from liquid and deploying some sort of flotation device

I’m late to the party here, but an additional reason that I didn’t see anyone else bring up already: spaceships realistically might ignore hydrodynamics if they only need to fly through space. Fictional spaceships are designed purely to look impressive, and a lot of them would move through the water like an anchor. Although more do look like aircraft or ships.

There is something along these lines that was almost real, but was never built.

Back in 1963, there was a proposal for the "Sea Dragon". While not submersible in the sense that a sub is, this massive rocket was 150 m (490 ft) long and 23 m (75 ft) in diameter and would have launched right from the sea.

It could carry an estimated 550 tonnes (540 long tons; 610 short tons) or 550,000 kg (1,210,000 lb) into low Earth orbit (LEO).

It's first stage would have been powered by an enormous 79,000,000 lbf (350,000 kN) thrust engine. Compare that to the Saturn V rocket, with 140,000 kg (310,000 lb) of payload to LEO and 7,891,000 lbf (35,100 kN) of thrust.

Because it is full of air

It is like trying to submerge a balloon, and the thrusters just aren't powerful enough.

A long haul spacecraft needs to provide food and water and deal with waste, and this problem is solved by onboard farms, where plants and fungi absorb the waste, make food, make oxygen, and generally keep everyone alive. This requires a large volume of air.

At the same time, the craft will be designed to be as light as possible, so the hull of the craft might not be very heavy.

The end result is that it's overall density is 1/5 of water, so it's engines would need 4x it's weight in thrust to go underwater. But 4G is rather unpleasant and won't make you much faster due to fuel/reaction mass constraints, so the thrusters simply aren't that powerful.

Edit: Since ArtisticPhoenix mentioned fuel, I thought I would look up the density of that. Liquid oxygen is slightly denser than water, at 1.141 kg/L, but liquid hydrogen is very light, at 0.071 kg/L. In the correct proportions, that's an overall density of 0.427. Now a spacecraft should be able to push itself underwater with that sort of density, but it is clearly not the right vehicle for the job.

Submarines (and all water-borne vessels) have a carefully-designed buoyancy. They must be no more dense and no less dense than water.

Submarines have ballast tanks (to manage their buoyancy).

They have have a suitable propulsion system -- e.g. propellers, a rudder, trim tanks (to govern attitude), and a hydrodynamic shape.

Not to mention instruments (sonar and so on).

And pressure (already mentioned in other answers).

They coud be submersible, but only if they were designed to be.

The only thing that is inherently suitable about a spaceship is that it's air-tight.

Any spacecraft that is designed for both atmospheric and exo-atmospheric use must essentially be built along aviation lines - where mass-limitation is the key. Under any real-world physics, getting mass up to escape velocity is very energy intensive, which means that any grams saved are worth saving.

Spacecraft must withstand many things; but certainly when it comes to transiting Earth-like planets (and the space between them) high pressure isn't one; just enough to hold around 1 BAR. Submarines on the other hand are incredibly heavy as they have to withstand far more pressure. For example, the Kilo-class submarine and the International Space Station are both around the same size (~70m) but the Kilo-class weighs around five times as much (2000-2400 tonnes compared to 400 tonnes).

TL;DR - unless you have an exceptionally compelling reason why the spacecraft would need to go underwater and to space (rather than having two separate vehicles) then it wouldn't be worth the huge compromises.

Because it's not designed to, and it wasn't deemed a worthwhile cost to adapt the design to do so.

Broadly, a spaceship's job (particularly one that flies in the air and in space) is to hold air inside the ship and resist, say, heating and atmospheric forces. Unlike a submarine, it doesn't have to cope with high external pressures or immersion.

This lends itself to some design simplifications- external pressure requirements are much lower, and you can shroud water-susceptible components (against rain) rather than sealing them in. External access panels can be added for ease of maintenance. Heat ablation tiles probably come off easily for replacement.

All these things will be selected without much regard to submersion, and as a consequence a dip in a lake (while unlikely to be completely fatal) is likely to cause no end of headaches for the crew. And don't even think about oceans - if they're anything like ours the salt water will do a real number on the ship from mere immersion, to say nothing of trying to dive like a submarine.

It depends on the universe.

The problem with spaceships going underwater is that they are usually built to do only one thing. One of the most famous scenes from Futurama is when the crew's spaceship sinks into the ocean:

Prof. Farnsworth: Dear Lord, that's over 150 atmospheres of pressure!

Fry: How many atmospheres can this ship withstand?

Prof. Farnsworth: Well it's a spaceship, so I'd say anywhere between zero and one.

However, there are plenty of spaceships in fiction which are built for higher pressure levels. Here are just a few examples. This list is by no means exhaustive.

The Leviathans, biomechanoid ships in the Farscape stories, were able to survive going and maneuvering underwater while not being exactly pressure–tight from the outside.

In X-Com: Terror From The Deep, the aliens assaulting Earth live on the bottom of the oceans. The final base to be stormed is at the Mariana Trench. Their ships work both abyssal depths and in space.

The Deep Angel Supercav online sci fi series had supercavitating fighters that could be deployed both in space and underwater.

In Michael Crichton's Sphere, a spaceship from the future is sunk at around 300m, but still manages to go to space.

In the Star Wars universe, the Trident-class assault ship can travel underwater and in space.

In the Masters or Orion series of videogames, the Trilarians are an aquatic race that builds their cities underwater - therefore their ships are launched from water to space.

In Flight of the Navigator the ship Trimaxion Drone Ship goes underwater.

And so on, with more and more underwater scifi being added every year.

There's a few potential reasons for this. I'm going to be making a couple of basic assumptions here, namely that the people on these ships are your typical oxygen-breathers from reasonably Earth-like planets.

Shape and Propulsion

Spaceships are, by and large, going to be out in space. They don't need to worry about aerodynamics unless they're going for atmospheric entry, which is at best a minority of what they're doing. Assuming a standard Earth-like planet, water is several orders of magnitude denser than air, which means streamlining suddenly becomes critical if you want to move underwater with any speed. A properly streamlined spaceship is hardly impossible, but it's going to get in the way of optimizing for cargo/weaponry/engines/etc., which is a point against doing so without a good reason.

There's also the problem of going anywhere. As I just said, you can't really go fast underwater, simply due to the need to move the tremendous mass of water in front of your vessel (multiplying the force required). I can't predict what's going into the engine of your spaceship, but it's probably something extremely high-energy; to be able to get off a planet and into space, you need power. I don't know what it would do to be firing engines like that underwater, but I strongly doubt it would be good for the ship to have that much power trapped right near the engines (evaporating who knows how much water and probably creating a shockwave from the sudden expansion) any more than it would help any unfortunate ocean life near the area.

Pressure

Spaceships are designed to retain atmosphere: they're designed to resist pressure from within, as an explosive decompression is obviously undesirable. Entering the atmosphere reverses that strain, but that's a reasonable thing to design for. Entering the water? Going underwater far enough to submerge your spaceship (assuming we're talking something bigger than a one-man fighter) is going to put several atmospheres of pressure on the exterior, a strain it probably was never designed to withstand from that direction (being designed to withstand a single atmosphere of pressure from within). You're going to spring leaks pretty fast, especially if you want to dive more than a hundred metres or so underwater.

Need

Generally, machinery is specialized: it's made to do a specific job and do it well. Trying to make one machine (your spaceship, in this case) do too many things at once will make it exponentially more expensive and probably be inferior to using various specialized machines for the tasks at hand (in this case, using a proper submarine or other such vessel for underwater exploration and leaving outer space to the spaceship).

This is probably the most important reason of all: there is no real reason to spend all the extra credits on making your spaceship capable of diving when you could spend those credits on a suitable submarine for the purpose and still have some left to improve your spaceship for other purposes (like adding a cargo module to your spaceship to hold said submarine). The economic case doesn't really exist.

Spaceships are not supposed to withstand a lot of external pressure

Have a look at our sister site Space.SE and the question Do spacecraft have similar structural integrity requirements as submarines? for some information about this problem. Here are a few quotes relevant to this question that come from the answers:

Next, the orbital craft. To get there it must be be light. A mild kick could have pierced Apollo's walls, ISS is more sturdy but still it's to withstand 1 bar pressure difference towards the outside (that's equivalent of mere 10m submersion depth), and again - towards the outside, that means no need for cross-beams to prevent buckling; it has natural tendency to bloat like a balloon.

The basic problem is that a submarine is supposed to go quite deep and withstand the pressure of all the water and atmosphere all around it - while a spaceship is supposed to withstand all the pressure from within from going outside.

Spacecraft are designed to contain internal pressure of not more than one atmosphere; submarines are designed to withstand dozens of atmospheres of external pressure.

The difference in requirements are big.

The structural members of a spacecraft hull are predominantly operating in tension, at a significant fraction of the material's yield limits, and the most likely failure mode would be tensile fracture. The structural members of a submarine hull are predominantly operating in compression, and the most likely failure mode would be buckling.

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For some interesting twist on your question you might also want to check out a question on WorldBuilding.SE: Would a submarine make a great spaceship?. The answers give some interesting insight into problems with the other way around, such as risky pooping (I think that's the biggest and by far most hilarious problem outlined in the thread).