The save slots are huge and include a ton of cached content. Certain areas in the game world rely quite heavily on these caches and create performance issues after a while. Parts of the Kelp Forest are at the top of that list.
Go to \Steam\steamapps\common\Subnautica\SNAppData\SavedGames\yoursaveslot (replace the last with the actual folder name) and delete these folders: CellCache and CompiledOctreesCache. Might want to back up the save first.
I do this whenever the game begins to stutter or slow down in any way, and it seems to help. Dialing down the visual settings also helps a lot in my case.