Sometimes I come across chests that are far in the water. Not on the ground of the water, just very far away from land. If it would be an iron chest I could just use the magnet ability to get it, but this does not work with wooden chests. The only way I was able to get the chests was to repeatedly swim against the chest, but this only moves it extremely slow. Is there any trick to get wooden chest out of the water?
If a chest is wooden, far out into a body of water or both you can use the Cryonis rune to raise chests out of the water. Aim the rune right underneath the chest then jump onto or climb onto your cryonis pillar. If the chest is far out into the water and you can't cast your rune due to the fact you're swimming just build of chain of cryonis pillars to the chest then raise a pillar underneath it.
As the other answer says, Cryonis is probably the easiest way to get the chests.
Keep in mind though that the wooden chests are destructible, so another way that you can get the loot from them is to destroy the chest then, chase down the stuff that falls out.
This is less useful because if the contents of the chest don't float, then you will have to fish them out with magnesis anyway.