One of the most unexpected harmful things we do to the integrity of marine ecosystems is transfer organisms around the world by ballast tanks of the Marine Shipping Industry. This article on how a mapping system might be used to combat this problem may be useful:
Shipping map helps combat introduction of Invasive Species
Other references on this website address the issues of introduced or alien species that we have to be on the lookout for affecting our coastline:
Invasive Alien or Introduced Species In Metchosin