PORTLAND – The floodwaters that caused millions of dollars worth of damage last week across York County also pose dangers to marine creatures and other wildlife along the coast.

While various pollutants in storm runoff are fouling coastal ecosystems, the most immediate threat comes from all the fresh water that is lowering the salinity levels in bays and tidal rivers.

“Fresh water is actually toxic to marine life if they can’t swim away from it,” said John Sowles, an ecologist with the Maine Department of Marine Resources.

The prolonged storm dumped so much rain that coastal estuaries where fresh water and salt water meet have become more like freshwater lakes whose salinity levels have dropped to near zero. More noticeable to the eye is the brown plume of stormwater over the ocean.

“It goes almost six miles offshore,” said Kittery lobsterman Steven Taylor. “It’s some murky.”

Taylor said it’s too early to gauge the impact on the lobster population, but he’s concerned that lobsters and other marine life that could not move offshore quickly enough to beat the flood will succumb to the fresh water.

“The truth of the matter is going to be seen in the next few weeks,” he said.

Lobsters in deeper areas will be safer because fresh water floats on top of salt water.

Fish tend to swim to saltier waters out to sea, but the eggs they laid and the nests they created in estuaries may succumb to the changes in salinity.

“This year’s class of fish probably will not do too well. This kind of disturbance will not be too kind to fish eggs,” said Michele Dionne, research director at Wells National Estuarine Reserve.

Less mobile creatures such as sea stars are most vulnerable and may die in greater numbers. But clams and mussels can adapt to environmental changes by effectively shutting down and going below ground.

At Great Bay near Portsmouth, N.H., the salinity level is normally about 20 parts per thousand but dropped after the flood to 0.5 parts per thousand, which is “basically fresh water,” said Stephen Jones, research associate professor at the Jackson Estuarine Lab.

“A lot of organisms that live in estuaries are used to a change in salinity, but when it gets consistently low, it’s a problem,” Jones said.

Salinity levels will eventually rise as fresh water mixes into the ocean, but it will take time for all of the stormwater to drain into the ocean and for the tides to flush it away.

Sewage, sediments and various compounds flushed off roads, parking lots and lawns will have a more subtle and longer-term impact. “It all does add up,” Dionne said.

Of land animals potentially affected by the flooding, the New England cottontail rabbit is seen by some biologists as a particular concern.

The cottontail, a candidate for listing as an endangered species, lives in low-lying patches of York County that were flooded out, said biologist Karen Morris of the Maine Department of Inland Fisheries and Wildlife.

“Unfortunately, a lot of the places they have to move to are in a developed area or across a road,” she said, which puts the rabbits at risk to predators and motor vehicles.

Because there are only between 300 to 400 cottontails in Maine, the threat to the species is “a reason for concern.”