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Several cruise ships will be releasing their wastewater this week into Skagway waters, where that's not usually allowed. Federal and state environmental agencies say it's for a good cause.

The Environmental Protection Agency research vessel Bold is in Southeast this week to help Alaska water-quality regulators collect data on cruise ship mixing zones.

Several cruise ships volunteered to help with the research. The Royal Caribbean Cruises Ltd.'s Millennium will be the first.

Both cruise ship and agency officials said this research could contribute to the debate over mixing zones.

"It could help make our case, or it could hurt the case," said Richard Pruitt, environmental and public health program director for Miami-based Royal Caribbean."

The Alaska Department of Environmental Conservation limits the pollutants that large cruise ships can discharge with their wastewater. That pollution is measured right at the end of the wastewater pipe.

The Alaska Cruise Association, an industry group, is appealing the standards, issued as a general permit in March. Cruise ship representatives say pollutants should be measured some distance from the pipe, after the treated wastewater has had a chance to dilute in the surrounding sea water.

State water quality regulators based pollution standards on computer models of how pollutants dilute once they're released into sea water.

"I'm excited to have an opportunity to get real field data," said Denise Koch, DEC cruise ship program manager.

DEC plans to use the mixing zone data to check where the model may need tweaking, or confirm if it's on the mark, said DEC scientist Albert Faure.

The plan is to inject a fluorescent dye into the cruise ship's wastewater pipe, upstream from where it's released. By the time it gets out it will be fully mixed with the contents.

Then scientists on a small boat attached to the cruise ship's rear end will sample the water, both at the end of the pipe and at various distances from it. They'll use a fluorimeter to detect the dye and measure its dilution.

Skagway, said Koch, was chosen because the waters there are still and don't flush as quickly as other ports cruise ships visit. That is also why Skagway's harbor is closed this year to wastewater discharge.

In another study, scientists will collect data on the nutrients that are in wastewater. Adding nutrients - such as nitrogen and phosphorus, also found in fertilizer - to water can affect what will grow there, but the state doesn't regulate their discharge.

Down the road, that could change if data shows they affect sea life, officials said.

"Cruise ships' advanced wastewater systems are quite good at treating bacteria and other pollutants, but they're not as good at dealing with nutrients," said Ed White of the DEC cruise ship program.

On Wednesday, boat crew and scientists gave public tours of the Bold, which is the EPA's only ocean research vessel.

The vessel once chased Russian submarines for the U.S. Navy, said its chief scientist, Kennard Potts.

He got the EPA to buy it from the Navy after it was decommissioned, then gradually decked it out with a lab that, for all its fancy high-tech gadgetry, is built with old shipping containers and other salvaged parts.

Field equipment on board allows scientists to take samples from the ocean floor, send remote-controlled robot to collect images, take water samples at different depths, and analyze it all back at the computer lab. The ship's scientist-divers collect samples in person, too, wearing thick suits to protect them from the toxic waste EPA regulates.

The Bold's scientists also have studied dredge disposal. They can scan the ocean bottom to find out whether dredge fill was dumped where it should have been, or test samples to see how habitat is responding.

• Contact Kate Golden at 523-2276 or kate.golden@juneauempire.com.