Keys are earned each time you level up in Splash. When you receive a key you can choose to use them either for unlocking a new species chest or unlocking a new area. Your keys will only be available to see by tapping either a chest or a locked area, but be careful not to accidentally place the key before you have decided if you wish to use it on this area, as it can not be moved.
You will only get a new key each time you reach a new level.