In my case I was holding the chainsaw (likely it's the same for all weapons or items that are in your hands at the time).

When you walk into the water, once the swimming animation starts, your item drops (just like ladders make your item drop). But then you can't retrieve it.

You can see the item in the world and you can see it in your local area via the inventory, just no way of picking it up as you're in a treading water/swimming animation.

Suggest one armed swimming animation? just anything that doesn't involve losing your item/primary forever.