The U.S. Environmental Protection Agency announced Wednesday that it has fined three Hawaii businesses and filed a civil complaint against another for operating large-capacity cesspools, which were banned a decade ago by the federal government.

Cesspools, which are used more widely in Hawaii than any other state, discharge raw sewage into the ground, where disease-causing pathogens and harmful chemicals can contaminate groundwater, streams and the ocean. The state Department of Health estimates that there are 90,000 cesspools statewide. Nearly 50,000 are on Hawaii island; almost 14,000 are on Kauai; more than 12,000 are on Maui; more than 1,400 are on Molokai; and more than 1,100 are on Oahu.

The 2005 federal regulations do not apply to single-family homes connected to their own individual cesspools or to smaller-capacity nonresidential cesspools.

EPA rules apply only to large-capacity cesspools, which are defined as those that discharge untreated sewage from multiple residential dwellings and from nonresidential locations that have the capacity to serve 20 or more people per day.

An estimated 3,292 of the 4,712 large-capacity cesspools that were operating in Hawaii in 2005 have been closed, many through voluntary compliance, since the ban was instituted.

“We understand that the cost can run $10,000 and up per cesspool and that this is not something that an owner can run out and do the next day,” said Dean Higuchi, press officer for the EPA’s Pacific Southwest region, which includes Hawaii, Arizona, California and the Pacific territories. “Generally, we try to put people on a compliance schedule. If they don’t make the changes in a reasonable amount of time, we can impose fines. Times will vary, but obviously we don’t want to give them 10 years since they’ve already had a decade to make the changes.”

Higuchi said the EPA’s latest crackdown on large-capacity cesspools has brought the count of enforcement actions in Hawaii to about 33, and has netted about $1.5 million in penalties.

“Cesspools serving resorts and restaurants can pollute the groundwater and nearshore waters where people swim,” said Jared Blumenfeld, regional administrator for the EPA’s Pacific Southwest region. “EPA is committed to protecting Hawaii’s precious water resources by closing down all large-capacity cesspools.”

The EPA recently assessed Travaasa Hotel Hana Resort on Maui a $187,500 penalty. The resort, which already closed a number of its cesspools over the last three years, also agreed to close its remaining 14 large-capacity cesspools within the next two years and replace them with state-approved septic systems. Vacation Inns International, which operates as the popular surfer’s vacation rental Backpackers Vacation Inn & Hostel on Oahu’s North Shore, will pay a $40,000 penalty and has agreed to close its six cesspools.

Shaka’s Pahoa LLC, which operates Pahoa Cafe nightclub, will pay a fine of $82,425 and has closed one cesspool and has another remaining cesspool to close.

In addition, the EPA has filed a civil complaint against landowner Keith Ward of Waimanalo for operating two illegal cesspools that serve Serg’s Mexican Kitchen.

“Eliminating 70 percent of the large-capacity cesspools in 10 years is a pretty good record, but we estimate that we’ve got 1,420 left,” Higuchi said. “We’re going to go through that list aggressively. More enforcement actions are pending.”

SharLyn Foo said the ban on large-capacity cesspools is an immense burden for Backpackers Vacation Inn & Hostel, the vacation rental business that was started by her late brother, well-known surfer Mark Foo.

“My plantation village vacation cottages were built in 1946. I’ve spent thousands of dollars trying to bring them into compliance,” she said.

While EPA regulations are only concerned with large-capacity cesspools, the state Department of Health views cesspools as substandard systems that threaten Hawaii’s public health and natural resources. The department is working on rules that ban new cesspools from being built. According to the department, Hawaii is the only state that still allows for the construction of new cesspools, and some 800 are installed each year throughout Hawaii island, Maui and Molokai.

The department also is writing rules to implement a tax credit program passed by state lawmakers last year that provides incentives for qualified single-family homeowners to replace cesspools.

Said state DOH spokeswoman Janice Okubo, “There are over 6,600 cesspools that are located near a drinking water source or within 200 feet of the shoreline, a wetland, or a perennial stream channel in Hawaii that may qualify for an upgrade tax credit.”