A new study by federal scientists has found that discharge from a sewage treatment facility in West Maui for years has been drastically undermining the coral reefs off Kahekili Beach Park.

The pollution is not only eroding the reef, but inhibiting new coral growth, according to the U.S. Geological Survey study accepted for publication in the Journal of Geophysical Research: Oceans.

But Maui County spokesman Rod Antone said Friday that the findings contradict data from other studies that show the coral reef at Kahe­kili actually getting healthier.

The question of whether coral reefs are being damaged by sewage from Maui County’s injection wells has been the subject of litigation and out-of-court negotiations for nearly a decade. Even before that, conservationists suspected the wells were linked to algae blooms plaguing the area.

Then, in 2013, a scientific study found that sewage from the Lahaina wastewater treatment plant is indeed finding its way into the nearshore waters, prompting U.S. District Judge Susan Oki Mollway to rule on two occasions that the use of the wells violates the federal Clean Water Act.

The county appealed to the 9th Circuit Court of Appeals, and attorneys on both sides argued their case before the court last month.

In an earlier settlement the county agreed to pay a $100,000 fine and spend $2.5 million for infrastructure designed to reuse the wastewater if the courts uphold the District Court ruling.

Opponents of the county’s sewage treatment practices have asserted for decades that the nutrient-rich sewage injected into the ground eventually winds up in the ocean, killing coral and triggering algae blooms, which deplete the oxygen in the water.

“We’re hopeful we will win on appeal,” said Earthjustice attorney David Henkin, who is representing the Hawaii Wildlife Fund, the Sierra Club Maui Group, the Surfrider Foundation and the West Maui Preservation Association.

Meanwhile, Maui County continues to assert on its website that there is no proof that the nutrients from its injections wells are the sole or most significant source of reef damage.

“While independent studies detected injection well discharge in some areas of algae blooms, other sources from rainfall runoff, reef siltation, agricultural fertilizer, over-fishing and human interaction must also be analyzed as contributing causes. It is important to thoroughly consider and identify all sources so that efforts to eliminate damage are successful,” according to the county’s injection well FAQ page.

In the new study, however, the wells that inject roughly 4 million gallons of treated sewage into the ground near the ocean each day were identified as a huge problem.

The results of the study, led by oceanographer Nancy Prouty of the U.S. Geological Survey’s Pacific Coastal and Marine Science Center in Santa Cruz, Calif., are being held up as another example of how land-based sources of pollution can negatively affect coral reefs already under attack by warming oceans, bleaching and ocean acidification.

The researchers found that corals closest to groundwater-leaking seeps (containing nutrient-rich sewage) grew slower and exhibited more “bioerosion” compared with corals farther away. These corals were pitted and riddled with holes, indicating they were victims of algae-loving creatures that gouge into the coral structure.

Coral reef bioerosion rates were much greater than predicted, according to the study, suggesting that nutrients worsen both ocean acidification — the ongoing decline of oceanic pH levels — and coral bioerosion, and that a collapse of the reef ecosystem would likely occur much sooner than previously expected.

“Our results confirm how valuable nearshore coral reef ecosystems — the cornerstone of Hawaiian tourism, shoreline protection, and local fisheries — are affected by land-based sources of pollution that are also magnified by effects of coastal acidification,” the study said.

The reported added, “With many of Maui’s coral reefs in significant decline and recent coral bleaching events leading to increased coral mortality, reducing any stressors at a local scale … is imperative to sustaining future coral reef ecosystems and planning for resiliency.”

Henkin said that when he saw the study Friday, he sent a copy to the state, hoping officials would take regulatory action against the injection wells.

But Antone said the authors of the study apparently failed to address significant land-based sources of nutrients that also easily find their way into the ocean during rainfall and through natural groundwater migration, including fallow agricultural fields and roads, private cesspools and septic systems.

In addition, a report written last month by aquatic biologist Russell Sparks of the state Division of Aquatic Resources indicated that reef fish and corals are making a comeback in the Kahekili Herbivore Fisheries Management Area, which was established in 2009.

Recent surveys show that earlier declines in coral cover have stopped and that there are signs of recovery with “greatly improved conditions for local corals to thrive,” Sparks wrote in the report that appeared in the Lahaina News.