Ships carry ballast water to manage their stability with different cargo configurations. When they pick up ballast water in one port and carry it to another, they also can carry along species that haven't previously been present in the destination port. These invasive species can cause a lot of problems.
Researchers at the University of Michigan are working on a "ballast-free" ship to discourage this sort of hitch-hiking ('Ballast-free Ship' Could Cut Costs While Blocking Aquatic Invaders, ScienceDaily, March 27, 2008). The system works by continually exchanging ballast water so that the water in the ship is always local: