Do I need to pass customs if I enter by swimming over a body of water?

Of course, why not? Note that a somewhat related, and much more common, situation does happen regularly as people move around with private crafts. In that case, it's up to you to follow all relevant rules and to report to the authorities within a certain time (usually it's understood you can at least dock to the harbor and walk up to the relevant office so you have already set foot in the country before getting clearance but you shouldn't wander around).

In a way, you could consider border checkpoints and all other enforcement measures as a convenience that helps travelers respect the rules but the mere fact that a border is not guarded does not exempt you from anything.

Where you come from during a particular trip also should not generally make any difference, countries typically define rules about entry, import duties, etc. independently of each other. While both typically happen in quick succession, the relevant event is entering the country, not leaving another one. Therefore, I see no reasons why you would be exempted by virtue of having transited through international waters.

Also, in many places where you would consider long-distance open-sea swimming (e.g. the English Channel), there are rules about safety and the like that would seem to be a more pressing concern (e.g. I believe than the French authorities do not allow swimming from their side so all recent crossings start from England). Realistically, you would secure authorization in advance and travel with an escort (a kayak to keep you company and a larger boat to make you visible, provide food, etc.) At the destination, authorities will be warned and might wait for you on the beach or wherever you plan to arrive.

Swimming over a random body of water to cross a border may simply be illegal without express prior permission from the border authorities - the question isn't "do I need to pass customs and have all the ordinary documents" (yes, you do), the question is "under what circumstances is this allowed at all".

Depending on the particular country, crossing a border in any spot that's not an explicitly allowed crossing point (both over water or ground) may be a crime that would get you detained and deported, or worse.

There is no basic right to simply travel across borders - you may only do it in a manner that both relevant countries allow, and they may (and do) place arbitrary restrictions, so ask the specific authorities of that country first. It's very likely that it would require prior registration and permit in order to do that legally.

Ship traffic has specific legal rules - if you've arrived on a ship from abroad and docked somewhere, it doesn't neccessarily mean that you're allowed to arbitrarily go on shore (or bring any goods) from the ship; but that's probably a different question.

There are some countries that allow for customs by mail for this type of crossing. For example, crossing into Canada via swimming or canoeing into the Quetico qualifies as a remote border crossing (link) because there simply are not customs offices in the middle of the wilderness. You still have to "pass customs" but you would not be arrested on site when you cross over, as you are pre-cleared for entry.

Passing into the US through the Boundary Waters Canoe and Wilderness area requires you to report to a customs office within a certain number of days of entry, so there is some leeway given, but ultimately you need to declare what you are bringing in to the country to the proper authorities.

If your swim is official and publicized, customs officials will be waiting for you on the shore. I understand this happened for people swimming Lake Ontario from the US to Canada, and for channel swimmers. I saw this for the man who recently tight-rope-walked above Niagara Falls - even before his family hugged him, he got his passport stamped. I believe Diana Nyad, who swam from Cuba to Florida, also had a photo op passport moment.

If the question is, can you sneak into a country by swimming across a border, the answer is yes, just as you can do by sneaking across a land border. But you would be in major trouble for doing so. Part of making the plans and arrangements for a long distance swim is contacting authorities and getting permission to land where you plan to land, and either to be met by immigration or to commit to getting yourself to an office as soon as you reach the shore.

There are answers stating that you can enter the given country only in the specified points. In the free movement zones, like Schengen, it's possible you can cross border anywhere (depending on the agreement between parties) but generally, you can't just enter the foreign country wherever you want.

But your problem can start even sooner, because first you enter the internal waters of the country, without permission and without registration. The registration rules apply to vessels, so entering it by the swimmer would be problematic. Even if you'd apply for the permission, it would be likely to be refused because of the problems with classifying you.

Unauthorized entering of internal waters of foreign country is something you should prevent in any case!

Suppose you survive, you'd be handled as a person illegally crossing the border. The legal actions depend on the jurisdiction and the mood of the officers. A Polish mountaineers group has illegally crossed the border between Poland and CCCP in Soviet times and they were deported back to Poland after spending night in police arrest, but it could end much worse.

Please take into consideration also, that Border Guards are usually armed!

This is one of those questions that can be answered by just asking yourself, "If it was legal, wouldn't everybody be doing it?"

Like, here in the U.S., drug smugglers go to huge efforts to sneak drugs across the border, and we have law enforcement people who patrol the border trying to catch them. If there was no law requiring you to pass immigration or customs if you swim ashore, why would they go to all that trouble? They could just take a boat to 10 feet off shore, jump in the water wearing a life jacket stuffed with cocaine, and swim. They could wave cheerily to any coast guard or police officers who might be around as they did. Ditto for people who today are illegal immigrants. All they'd have to do is drive to a beach, swim out ten feet and swim back, and now they're legal.

I don't claim to be an expert on immigration law, but if there ever was such a loophole, I'm sure it was plugged many decades ago.