For total submersion you use parts that are sealed. The conductors of the connectors (charger, headphone jack) don’t let water through. They use non corrosive metals like gold, which don’t rust away when exposed to standing water.
The phone itself is sealed using rubber o-rings that prevent water from entering through the gaps where the enclosure needs to be sealed.
The speakers are connected to thin films that iirc are glued or otherwise sealed against the top of the enclosure so water doesn’t enter the electrical area.
There is some controversy over design decisions like the purported reason for Apple removing the headphone jack to make the iPhone water tight, which is kinda true because it removes a point of failure and kinda false because there were other reasons, like allowing more space on the PCB for them to increase the battery size, or making money from air pods. At the end of the day any feature as big as waterproofing requires so many changes to the enclosure and assembly that it drastically impacts every other aspect of the design.
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