The annual beach water quality report from the Natural Resources Defense Council indicates that Maine has some of the most polluted water in the country — but state officials and scientists decry the report’s methodology and conclusions.

“We just strongly disagree with this assessment,” Jessamine Logan of the Maine Department of Environmental Protection said Thursday morning. “We welcome Maine residents and tourists to our beaches, which are clean and safe and open for swimming over 95 percent of the time.”

That’s a different message than the one shared in the just-released report, which used monitoring samples taken in 2013 at nearly 3,500 coastal U.S. beaches. According to the Natural Resources Defense Council, 19 percent of the samples taken at 55 Maine beaches exceeded the Environmental Protection Agency’s new, suggested water quality standard for presence of pollutants, called “Beach Action Value.”

Nationally, 10 percent of all water samples did not meet this standard, according to the executive summary from the report, titled “Testing the Waters 2014.” Maine ranked 27th out of the 30 states included in the report, with only Mississippi, Alaska and Ohio showing greater percentages of water samples that exceed the new quality standard.

“Although protective beach water quality standards are critical, ultimately the most important long-term action to protect beachgoers is to adopt policies that address the sources of beachwater pollution, particularly stormwater runoff,” the report summary stated.

State officials suggested that numbers in the environmental nonprofit group’s annual report were skewed against Maine, where the beach season is very short, lasting only from Memorial Day to Labor Day. Additionally, 2013 was Maine’s wettest year since the Maine Healthy Beaches monitoring program began in 2003, according to coordinator Keri Kaczor. The 23 inches of rain that fell last summer was a record, and it seems to be part of a trend of the state having warmer, wetter summers.

“We do have issues when it rains,” she said. “We have a lot of water in Maine, with the rivers, the streams and the storm drains bringing pollutants from upland areas to the sea. When we have a wet beach season, we have problems.”

Kaczor said that in past years, the guideline used by the EPA and the environmental group’s report was 104 colonies of bacteria per 100 milliliters of water. This year, for the first time, the standard was lowered to 60 colonies per 100 milliliters.

“Yes, we have issues, but this report amplifies them,” she said.

In Maine, the communities that voluntarily participate in the Maine Healthy Beaches water quality monitoring don’t just take samples where people swim on sunny beach days. Monitors also sample from freshwater inputs — rivers, streams and storm drains — which are exactly where higher levels of the enterococcus bacteria are likely to be found. That is a bacteria found in the gut of warm-blooded animals, and while it doesn’t make people sick, it is an indicator that something else in the water may do so, according to Kaczor.

However, the testing doesn’t indicate the source for the bacteria, which would be most concerning if it was of human origin, she said. Maine beaches often are surrounded by marshes, with lots of birds and other wildlife, whose droppings contain enterococcus bacteria, but the presence of the animals indicate that the ecosystems are healthy.

Other officials around the state said that the ‘one size fits all’ approach of the Natural Resources Defense Council doesn’t work here. Jon Carter, town manager of Wells, said that Wells Harbor Beach, named by the council as the worst water quality offender in Maine, is a tiny beach located on a river.

During and after a rainstorm, it is more likely that this small beach will have higher levels of the bacteria, which DNA testing has shown comes mostly from animals, he said. Other beaches in a community known for its wide swaths of sand also are monitored and are not problematic.

“I think the hype is that you’re making more of this beach than it really is,” Carter said, the day after a rainstorm dumped an inch of water on the area. “It’s a quiet area to relax in, and it’s popular with the locals.”

Wells, like many other waterfront communities in the state, puts up an advisory sign after heavy rainstorms to let people know if there is an increased risk at the beach. The advisory sign was in place on Thursday, he said.

Brandy McCurry of the Webhannet River Boat Yard in Wells said that the tidal river is beautiful, as are the town beaches. She said she has personally conducted a cleanup of the beach and the waterfront, and collected a minimal amount of trash after covering a 2-square-mile area. While she was unfamiliar with the Natural Resources Defense Council report, she said that people in Wells feel they have clean water and beaches that are fine for swimming.

“I’ve never had anybody come here and say, ‘Oh, the water’s dirty,’” she said. “It never happens.”

Fred Dillon, stormwater program coordinator in South Portland, said that his city has gone to some extreme lengths to try to ferret out the source of the bacteria, which is not always an easy task. Earlier this year, South Portland hired dogs trained to distinguish between human or animal fecal matter and brought them to places such as the popular Willard Beach.

The dogs found “very, very low” concentration of human waste, he said.

“‘Where is this poop coming from?’ is the question,” Dillon said, adding that he is of two minds about the Natural Resources Defense Council report.

“I think it’s good that there are environmental groups trying to hold people’s feet to the fire,” he said. “But whether the [new] standard is better than the old one — I’m not sure that’s the case.”