After a heavy rainstorm in December, the water at the foot of a concrete-lined stream emptying into Maunalua Bay turned an ugly chocolate color. Over several hours, an estimated 20 tons of sediment and other pollutants washed into the East Honolulu bay, and the brownish-red plume extended seaward about the length of two football fields.

Much of the muck is still there today, settled along the reef flat. It is expected to remain for years, diminishing conditions for marine life along the shore. Worse, the muck will be kicked up again and again by wind and waves, an ongoing process that will harm the bay in ways not fully understood by scientists.

But this much is clear: Land-based pollution, including sediment runoff, is a significant contributor to the degradation of reefs at multiple spots around the main Hawaiian Islands. Some scientists believe it is the biggest threat in the near term facing Hawai'i's reefs.

The marine environment today is paying the price for poor land-use practices dating back decades and, in some cases, a century or two. Vast swaths of land were cleared for agricultural purposes. Entire hillsides were denuded by grazing animals, contributing to serious erosion problems that persist today. Wetlands, flood plains and other areas that functioned as natural percolation systems to filter pollutants from surface runoff were paved over to make way for development. Now, much of the muck that once was removed from the water flows into the ocean.

As more of the coastal areas were developed, streams also were straightened, and some were lined with concrete for one primary purpose: to protect against flooding by moving huge volumes of rainfall from land to sea as quickly as possible.

The problem, scientists say, was that little attention was paid to how all the changes might affect the reefs, the backbone of Hawai'i's marine ecosystems.

"Our past practices treated the coast as a dumping ground," said Gerry Davis, assistant regional administrator for the National Oceanic and Atmospheric Administration in Hawai'i. "In the end, we've taken our coastal problems and put them at sea."

DATA SCARCE

Today, scientists know much more about the effects of land-based pollution — especially excessive sediment runoff — on the reefs, although little hard data is available showing how much damage such pollution has caused in Hawai'i. Studies continue at specific sites.

But general effects already are well known.

Tons of suspended particles turn coastal waters into a muddy mix, blocking sunlight from reaching living corals along the ocean bottom. The marine organisms need sunlight to survive.

Layers of sediment also settle directly on the corals, essentially smothering them, and the mud likewise covers portions of the ocean bottom, preventing new corals from growing there. The runoff also affects other marine organisms, throwing the nearshore ecosystem out of whack.

Because the sediment, once settled, is stirred up again by wind and waves, a process that is repeated regularly over long periods, the damage to the reef ecosystem is magnified many times over. Mike Field, a California-based U.S. Geological Survey scientist studying the runoff problem on the South Moloka'i reef, found that one kilogram of sediment discharged into the water had the impact of roughly 3,000 kilograms because of the re-suspension effect.

"Sediment is the death that keeps on killing," said Bob Richmond, a University of Hawai'i marine biologist.

COMPLICATIONS

Land-based pollution is only one of multiple factors that contribute to reef degradation around the main Hawaiian Islands. Overfishing, invasive species and climate change are among the others, and all can play a role simultaneously, making it difficult to pinpoint the cause of a reef's demise. Still, some scientists believe overfishing is doing more harm to Hawai'i's reefs than pollution, though many fishers dispute that.

Excessive sediment runoff and other land-based pollutants tend to affect mainly protected coastal areas, such as bays, where the water is shallow and circulation poor. Such conditions prevent the suspended particles from being quickly flushed to the open sea.

Indications of pollution-related degradation are evident in many coastal areas around Hawai'i. Maunalua, South Moloka'i, Kaho'olawe, Lana'i, Honolua on Maui and Hanalei Bay on Kaua'i are among the affected areas.

At Honolua, for instance, coral cover has plunged from 42 percent in 1995 to 9 percent in 2005, and increased sedimentation, chemical runoff and other types of pollution are suspected of being major factors, according to researchers monitoring the area. Invasive algae are scarce at Honolua.

For each area believed to be hurt by land-based pollution, many others seem unaffected. Because sediment settles primarily on the reef flat, where water quality typically isn't as good as farther offshore, and coral cover is much less, the impact is largely confined to the flat, some scientists say. For the most part, the reefs farther offshore — where they crest, then slope into deeper waters — are more lush and healthy.

"Is (land-based pollution) some ongoing problem affecting all of our reefs? No. It only affects a small part," said Marlon Atkinson, a UH professor at the Hawai'i Institute of Marine Biology.

But the concern among many scientists is that most of the coral ecosystems around the main Hawaiian Islands are at risk, and that damage from pollution slowly is expanding as more pollutants enter the ocean and urbanization continues to spread. Scientists also point out that they still are learning about the effects of such pollution, and some long-term impacts may not be evident now.

"Is the sky falling? In my opinion, no, because these systems are quite resilient and recoverable," said Davis, the NOAA official. "But at some point, if we don't do something to correct the problem, we'll end up with systems that are not recoverable."

VISIBLE DAMAGE

A hint of the spreading damage is found off South Moloka'i, where one section of an otherwise lush sloping reef, called the fore reef, is devoid of coral cover. Field, the USGS geologist, believes the lack of coral is related to the constant flushing of muddy water from decades of heavy soil erosion.

Similar worries extend well beyond Moloka'i, he said. "Land-based pollution is probably the major (reef) concern in Hawai'i."

While the effects of excessive sedimentation on corals generally are well known, less is known about the impact of other types of pollutants, such as pesticides, fertilizers and excessive nutrients.

Evidence from ongoing studies on Maui show that pollutants from two large sewage injection wells and other sewage-related sources appear to be significant factors in causing algae blooms off Lahaina and Kihei, according to Celia Smith, a UH botany professor who is among the researchers doing the work. Fueled by excessive nutrients from the sewage systems and a reduction of fish that graze on seaweed, the algae are overtaking large sections of the reef.

The research is the first to show that pollutants from the injection wells, cesspools and septic tanks have made their way to the coastal waters and are affecting the reefs. That raises additional concerns in part because Hawai'i has more cesspools — roughly 100,000 — than any other state.

"There may be many other subtle effects that will take more science to document and understand," Smith said.

FENCES SAVE REEFS

As scientists learn more about the impact of land-based pollution, government officials are trying to do more to reduce the problem.

Stressing the link between land and sea, plans are in the works or have been implemented to alter property uses and consumer practices to reduce the discharge of pollutants into streams, storm drains and the ocean.

Fences, for instance, have been installed on mountains around the state to prevent feral goats and other grazing animals from turning vegetation-lush slopes into denuded wastelands.

The Army Corps of Engineers is considering alternatives to hardening streams that will not only prevent flooding but better protect the marine environment.

For streams and other outlets that are considered impaired, the state is developing maximum thresholds for pollutants, including sedimentation runoff and other contaminant's that do not come from industrial or sewage treatment plants. (Those are called nonpoint source pollution).

Once those maximums are set, the state works with landowners to try to stay within the thresholds, though compliance in the nonpoint arena largely is voluntary because of limitations with the law and because pinpointing the source and impact of the pollutants can be difficult.

While land-based pollution is getting a lot of attention now, Hawai'i's approach to managing and protecting its marine resources is so fragmented and lacking basic data that many say they are skeptical about outcomes.

Chip Fletcher, a UH coastal geology professor, says Hawai'i is the only state without a centralized science office to deal with such issues as coastal erosion.

"If you were designing an expensive system to fail, this is what you would come up with," Fletcher said.