How do boats affect the environment?

The noise and motorized functions of boats can disrupt wildlife and the environment, and the waste generated by boats can also be harmful to the environment. Boat propellers can also kill animals in ocean water.

Another perspective: More, now than ever, the public eye is focused in on the environment. With this call to action, cruise lines have stepped up to the plate to care for the environment in ways you may not expect.
A world-wide agreement in respect to protecting the oceans and environment called MARPOL was passed defining the standards of environmental protection. Some of these requirements include:
Requirements for what can go overboard (virtually nothing except clean treated water and 'pulped' sorted food waste to feed the ecosystems.
Requirements for containing any spills and cleanup procedures.
What can and can't be burned on board. Currently some plastics and most paper and cardboard are incinerated on board. Other materials such as glass, metals, heavy plastics, medical waste, sludge (oil and black water) are offloaded and recycled or processed by shore-side vendors.
As far as fuel is concerned, it is necessary for large ships to keep engines on at all times, even in port, to keep lights, air, electricity, refrigeration etc. going. However, ships are constantly upgrading fuel sources and fine-tuning engines to ensure the cleanest possible burn. Furthermore, the future of cruise ship ports may include an opportunity to connect to shoreside power, which would allow them to power down onboard engines and reduce emissions even further.
All cruise lines understand and respect the environment. There's nothing special about taking a cruise if the oceans are filled with waste and pollution all of the time, right?