They pour into Seattle by the hundreds of thousands: cruise ship passengers from all over the world, clamoring to board floating cities for slo-mo luxury tours of Puget Sound and points beyond. Seattle has become a major launching spot for cruise ships setting sail to southeast Alaska, with its cavorting whales, calving glaciers and staggeringly beautiful snowy-mountain vistas. Alaska is such a popular destination nowadays that Disney Cruise Line is getting into the game; beginning this spring, Disney will join other major lines—Holland America, Norwegian, Carnival, Celebrity, Princess and Royal Caribbean—to dock their behemoth waterborne hotels in Seattle.

So what does that mean for the already pressured, ecologically significant waterways of Puget Sound, the nation’s second-largest estuary (behind Chesapeake Bay)? According to the state agency Puget Sound Partnership, the body of water is already hard hit on numerous fronts with contaminated runoff from streets and industry; failing septic systems; and an increase of housing developments covering hillsides that were once forested land. The group estimates that billions of dollars are needed to clean up the Sound and restore it to better health. But, like those of most government programs, funds for the project are being cut; the Puget Sound Partnership will have to shave off 10 percent of its budget for 2012.

That could make it a pretty big deal for yet another cruise line to begin operating here. Cruise ships are basically floating cities, complete with a city’s big-time concerns, such as sewage, trash and air pollution. A typical one-week voyage can produce hundreds of thousands of gallons of sewage; millions of gallons of gray water from sinks, kitchens and laundry facilities; and tons of trash, according to the national environmental advocacy group Friends of the Earth, which tracks the cruise ship industry. The ships also kick out pollutants like sulfur dioxide and nitrogen from their enormous engines.

“The dirtiest fuel on the planet is burned on cruise ships: bunker fuel,” says Marcie Keever, oceans and vessels project director for Friends of the Earth. “Bunker fuel is thousands of times dirtier than on-road diesel truck fuel. It’s so heavy, it’s in almost a semi-solid state.”

Sounds bad, but those who monitor the health of Puget Sound say it might not be too bad, if—and it’s a big if—Disney and all of the other cruise lines continue to make running clean a priority. Both increasing regulations and voluntary efforts by the cruise lines are improving the environmental picture, Keever says. The Port of Seattle has installed a shore power infrastructure at Pier 91 that allows cruise ships to plug in at the docks, rather than run their engines. “The power supplied by ports on the West Coast is considerably cleaner [than running engines], with air pollution benefits,” Keever says.

That’s good news to Kimberley Cline, spokeswoman for the Puget Sound Clean Air Agency. “We are definitely pleased to hear the Disney ships will use shore power when berthed,” she says.

But Congressman Jim McDermott (D-Seattle), who has pushed for tougher environmental regulations regarding cruise ships, sounds unconvinced. “These ships release thousands of gallons of sewage, garbage and wastewater into our waters,” he says. “Before these lines start running, I would like to see Disney—and other operators—commit to ensuring a clean operation that will ensure the long-term health of the Sound and coastal waters.”

The cruise lines all say they have done just that, adhering to federal regulations that require the ships to discharge their dirty water outside of Puget Sound, in open ocean, a minimum of three miles from shore. When in international waters—cruising past Canada, for instance—ships must be at least 12 miles out to sea. And Disney says it goes a lot further, citing voluntary efforts focused on “utilizing new technologies, increasing fuel efficiency, minimizing waste and supporting conservation worldwide.” “We have dedicated environmental officers aboard each Disney ship [who are] responsible for all recycling, waste minimization and environmental compliance,” says Bert Swets, vice president of marine and technical operations for Disney. “We were also the first in the industry to apply a special eco-friendly hull coating to our ships.”

According to Friends of the Earth, Disney is doing a better job these days of addressing environmental concerns, earning a “most improved” rating on the group’s annual cruise line scorecard. “They retrofitted both their ships to install advanced wastewater treatment,” Keever says. “Disney is doing the right thing, and they’re going in the right direction.”

Another thing going in the right direction: Seattle’s bottom line. Those big ships mean big money, and it’s money Seattle really needs. The Port of Seattle reports that each ship steaming out of Seattle to Alaska leaves about $1.9 million in its wake, with its hundreds of passengers shopping, eating and staying at local hotels. In addition, in 2011, the cruise industry brought in $18.9 million in state and local taxes, and 4,447 jobs, according to the Port, and those numbers are expected to go up this year with Disney on board. The Port projects that a whopping 880,918 cruise passengers will take 201 scheduled cruise ship trips out of the city in 2012, from two ports (one downtown, at Pier 66, and one in Magnolia, at Pier 91). This hopping cruise industry is “a critical component” of Seattle’s tourism industry, according to Seattle’s Convention and Visitors Bureau, and it appears on track to keep growing. According to the Cruise Lines International Association, an industry group that represents nearly all the major lines, Alaska is the second-most-popular destination (after the Caribbean) for cruisers.

Beginning on May 28, the Disney Wonder—a 964-foot-long, 83,000-ton temporary home to 2,700 travelers—will launch a total of 14 seven-night cruises from Seattle, steaming north to the scenic Tracy Arm fjord and the towns of Skagway, Juneau and Ketchikan, as well as Victoria, British Columbia.

Which could actually be an environmental plus, according to Tom Bancroft, executive director of the environmental advocacy group People for Puget Sound. “Disney has a great opportunity to raise the bar for the cruise industry here,” he says. “They’ve got an opportunity to provide environmental educational opportunities while on Puget Sound. I think the chance for people all over the country to get that perspective while on a cruise is just fantastic. We want to see people from all over country come and say, ‘This should be protected.’”