Thousands of Hartford-area water customers have been dealing with a boil advisory for two days as officials try to find out why micro-organisms have been appearing in water coming out of a treatment plant.

The organisms are not harmful, but their presence in finished water coming from the public water supply shows there is a problem with the system, state health officials said.

James Pines, an information technology project manager who lives in Bloomfield, spotted the problem Monday after he installed a $70 filter onto his home's main water line. He soon saw what he called "little polliwogs" gather inside the cartridge.

"This is what we are drinking," he recalled Thursday. "We were disgusted. ... You shouldn't be drinking in little odd things."

The region's water agency, the Metropolitan District Commission, identified the organisms as harmless copepods and rotifers and said they were appearing in water coming out of a treatment facility in Bloomfield. The organisms are clear and about the size of a sewing pin head, the agency said.

The state health department and the MDC are investigating to determine whether that problem involves improper filtration, a breach in supply or distribution lines, or some other problem with the way the water is stored and treated.

The MDC issued the water boil advisory Wednesday to customers in Hartford and nine surrounding towns, though it was called off for four of the towns on Thursday night. The water distribution systems in East Hartford, Glastonbury, Portland and South Windsor had been isolated from the reservoir where water containing micro-organisms originated, the MDC and the state health department said.

Customers in Hartford, West Hartford, Bloomfield, Windsor and parts of East Granby and Windsor Locks should continue to boil drinking water for one minute through the weekend, the agencies said.

"It's not harmful, but if they are found in your water, boiling for one minute would eliminate them," said Melissa Bengtson, an MDC spokeswoman.

Ice cubes and baby formula made with unboiled tap water should be discarded, but bathing, showering, hand-washing, teeth-brushing, laundry and dishwashing are fine without boiling the water, the MDC said.

Restaurants and schools are feeling the effects. The kitchen staff at Trumbull Kitchen, near Hartford's XL Center, had 25 gallons of boiled water chilling in the restaurant's coolers by midmorning Thursday in anticipation of the lunch rush.

The chef, Christopher Torla, also said he has 40 cases of water on order "to keep us ahead of the curve if this thing goes long-term."

The Peppercorn's Grill, on Hartford's Main Street, also plans to serve its customers bottled water until the boil advisory is lifted.

"It's a better safe than sorry kind of thing, but we have to be careful," said general manager Ryan Guerard.

The water fountains at the seven Windsor Public schools have been covered with plastic bags, said Superintendent Elizabeth Feser. But lunch is still on for the district's about 4,000 students: Chili cheese wraps were served to the elementary school students.

The MDC has raised chlorine levels at the Bloomfield plant and is hoping to lift the advisory by the weekend.