From a boat in the Potomac River, a blue flag was visible over the nearby Thompson Boat Center as Masaya Maeda used a long pair of metal tongs to dip a plastic bottle into the river and “grab” a water sample.

The blue flag meant that, when analyzed, samples Maeda had grabbed from the river the day before showed the river’s water was safe for boaters.

Depending on what the lab found in the new sample, the next day’s flag might still be blue — or yellow, warning boaters of bacterial contamination.

It’s all part of a program launched this summer by the Anacostia Watershed Society aimed at raising water quality awareness in the Potomac and Anacostia rivers by raising flags.

“Our hope is that we can educate water users about the problems, and also raise the level of concern, so we can hopefully achieve a solution much more quickly,” said James Connolly, executive director of the watershed society.

Although the Potomac and Anacostia have a host of water quality problems, the flagging program is aimed primarily at fecal coliform, a bacteria that stems from the presence of human and animal wastes and can cause illnesses in people.

One of the main sources of the problem is visible not far from where Maeda grabbed the sample: A giant brick tunnel — big enough to drive a small boat into — which is one of the 60 “combined sewer overflows” in the District of Columbia.

Like many older cities, the storm sewers that handle street runoff drain into the sanitary sewers, which treat wastes. During heavy rains there is more runoff than treatment plants can handle, and the excess — about 2 billion gallons of raw sewage annually — overflows straight into the Potomac and Anacostia rivers.

The district recently developed a plan to fix the problem, but it carries a price tag of more than $1 billion, and as of now is unfunded.

It could take 20 years to complete the project, Connolly said, and the group would like to build pressure for faster results — and more financial support from the federal government, which built the systems and owns much of the “sewershed” in the district.

Most people don’t understand how runoff affects water quality, and Connolly said the flagging program can help build awareness.

Every day since early June, Maeda, a biologist working for the watershed society, has taken water samples from four set locations, which are sent to a lab the same day for analysis. The signal flags are then raised at five boat houses and parks along the river.

The goal, Connolly said, is not to scare people from using the rivers, but to better inform them about water quality issues. “One of our missions is to promote usage of the river,” Connolly said. “Usage promotes stewardship.”

The boating standard for fecal coliform is 1,000 fecal coliforms per 100 milliliters of water (about a teacup). From June through early September, monitoring showed 12 violations of the standard. The yellow flags hoisted on those days are a warning to the growing numbers of boaters who use the river that it may be dangerous to come into contact with the water.

If there had been more rain — and therefore more runoff — the number may well have been even higher.

Connolly hopes the cautionary flag days on the river eventually get as much attention as code red ozone days, when people are urged to drive less and stay indoors because of high levels of air pollution.

The program is supported by an EPA Region III Environmental Monitoring Protection and Community Tracking grant aimed at using monitoring to increase public awareness of environmental problems.

“We hope that the flagging program will not only pique curiosity among local citizens about health-related conditions, but also stimulate a desire on the part of those citizens to learn about water quality and its effects on both human beings and wildlife,” said Rebecca Hanmer, director of the EPA’s Bay Program Office.

The flagging effort is patterned after a program created by the Charles River Watershed Association in Massachusetts that regularly tests river water at four sites. The results are reflected not only in flags flown at sites along the river, but are also published in local newspapers and on television.

In the Charles River program, high fecal coliform counts found in monitoring for the flagging program led to investigations that discovered a number of illegal sewer hookups discharging into the river.

Likewise, the Anacostia monitoring is revealing its own surprises. The greatest number of high fecal coliform counts thus far have not come from near the combined sewer overflow sites, but at Bladensburg. in Maryland’s Prince George’s County, where two branches of the Anacostia merge. That area is upstream of any combined sewer overflow discharges, but had seven violations — more than half of all those monitored.

Connolly said the source of fecal coliforms in that area is unclear. The watershed group has sent samples to Virginia Tech for DNA analysis, which should reveal whether they originated from humans or animals. That will provide clues as to where to look for the source of the problem.

Whatever the exact source, Connolly said, it has to be upstream of Bladensburg — not the district. “Maryland is a big player in the Anacostia,” Connolly said, “but we would like them to be more involved.”