Cleaning is a Skill which you can buy from the Bookstore. You need to use it on one of Your Crew to learn the ability. Once learned the Pirate with the ability will automatically begin cleaning by tossing overboard anything that causes low Morale.
However, while cleaning, the trash being flung overboard becomes a projectile that does disengage grapples and may knock your crew into the water. This will kill those without Swimming.