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Cruise ships are sometimes called "floating cities", and just like cities, they produce sewage, solid waste and toxic emissions associated with acid rain and global warming. According to Bluewater Network, people living near ports are at greater risk for developing respiratory illnesses and cancer. Tougher regulations are on the horizon, but it's hard to predict how effective they'll be. The industry is littered with examples of cruise lines that were fined for "circumnavigating" laws governing waste disposal.
If you're determined to travel this way, you should ask about the cruise line's wastewater treatment systems and waste management policy (for example, dumped at sea or disposed of after docking, recycled or not, etc.). Look out for biodiesel vessels in the future. While a biofuel mix (regular fuel and vegetable oil) doesn't eliminate all toxic emissions, it significantly reduces them. Cruise lines operating out of Vancouver have expressed interest in this option and AML Cruises have tested a biodiesel ship in Montreal's Old Port.