Water in the narrow channel at the north end of the Niantic River turned greenish-white and gave off a sulfurous odor Friday, prompting concerned residents to call local officials and the state Department of Environmental Protection to investigate.

"This morning there were eels and crabs all along the shore, gasping for breath," said Dave Smith, who lives in a riverfront house on the Waterford side of the tidal river, standing with his wife, Heide, along the shore. "You can see the water is discolored."

The state DEP crew that investigated the situation determined the discoloration and odor were the result of a natural phenomenon called "anoxic water," not a pollution spill. The Ledge Light Health District on Friday closed the northern part of the river above Sandy Point to swimmers and skiers and posted signs about the closure. The entire river has been closed to shellfishing.

Jeff Chandler, supervisor of the DEP's emergency-response unit, said the DEP collected water samples in the area from its marine-spill response boat that afternoon. The area is between the peninsula known as Golden Spur at the river's northern end, Oswegatchie Hills on the East Lyme side of the river, and Comfort Point on the Waterford side.

"We did find a low oxygen content in the water," he said. "It was further exacerbated by inversion of the water" when the bottom layer, which is particularly oxygen poor, mixes with the top layers. The odor, he said, is caused by decaying material.

Heavy rains ealier in the summer carried an overabundance of nutrients into the water, which sparked an algae bloom, according to Mark Johnson, DEP fisheries biologist. During the hot weather over the past two weeks, the algae died, and the decaying algae consumed a large amount of oxygen in an area that historically already has a low oxygen content.

The area also gets little water exchange with the rest of the river. The waters at the bottom are particularly low in oxygen compared to the upper layers, and the heavy rains probably caused some mixing, Johnson said. The same phenomenon has occurred in that area at least once in the last decade, he said.

In an e-mail message Friday, DEP Environmental Analyst Harry Yamalis explained the phenomenon to East Lyme First Selectman Paul Formica. It also occured in a tidal estuary in Stratford, Yamalis said.

Johnson expects the problems will clear up naturally over the next several days.

He and David Molnar, also a fisheries biologist, waded along the northern shore of the river Friday afternoon looking for any dead fish or other marine life, but found none. Numerous large blue crabs could be seen scurrying in the shallow water along the shoreline in some parts of that area, however. Johnson said the crabs and other animals were gathering near the shore in search of waters with more oxygen.

"I don't know how alarmed to get about something like this," he said. "The question in my mind is, 'How do land-use practices exacerbate this situation?' "

Stormwater runoff from a rainfall carries with it pollutants from fertilizer, pet waste, septic tanks, vehicles and other sources. Much of it is rich in nitrogen, which is a nutrient for algae and causes algae blooms.

Last year the four towns in the Niantic River watershed, which extends into parts of Salem and Montville as well as East Lyme and Waterford, began an effort to better manage stormwater and reduce pollutants flowing into the river.

The river is classified as an "impaired" waterway according to federal environmental standards because of excessive levels of bacteria, sediment, nitrogen and phosphorous.

j.benson@theday.com

Day staff writer Amy Renczkowski contributed to this report.