State aquatic biologist Bill Walsh was conducting an underwater survey off the Kohala Coast of the Big Island three years ago when he came upon "a dead zone" where a thick blanket of brown muck had settled on centuries-old coral reef.

"We couldn't even find the bottom. It was deeper than our elbows. It had dusted the reef, even the high portions of it," Walsh said. "We were flabbergasted that nobody had reported anything."

An investigation by the state Department of Health's Clean Water Branch attributed the pollution to two intense periods of localized flash flooding about a week apart in October 2006 that washed tons of dirt, tree branches, gravel and other debris into the ocean at three main points, Puu Kamalii Stream, Honokoa Gulch and Keawewai Gulch.

A contributing factor was the Oct. 15 Kíholo Bay earthquake, which occurred between the two downpours and loosened large amounts of soil and rock that slid into streams and gulches discharging into the ocean, according to the branch's report.

A survey of nearby construction activities found numerous instances in which "best management practices" for erosion control were not in use. At one site, recently grubbed and graded land was not stabilized and sloped toward Puu Kamalii Stream. Collapsed silt screens were observed at other locations, and fill material, construction waste and refuse had been dumped into gulches.

Culverts that run under the coastal Akoni Pule Highway proved inadequate to handle the sediment- and debris-laden flooding, and the overflow rushed across the road, collecting more dirt before emptying into the nearshore waters, the report said.

The Clean Water Branch ultimately found that while the construction activities may have contributed to the sedimentation episode, no individual culprits were responsible and that "nonpoint source pollution" was to blame.

Nonpoint source pollution is caused by rainfall moving over and through the ground, according to the U.S. Environmental Protection Agency. As the runoff moves, it picks up and carries away natural and human-made pollutants, depositing them into lakes, rivers, wetlands and coastal waters. The pollutants may include fertilizers, herbicides and insecticides from agricultural lands and residential areas; soil from improperly managed construction sites; oil, grease, and toxic chemicals from urban runoff; and bacteria and nutrients from livestock waste and faulty septic systems.

Clean Water Branch environmental health specialist Matthew Kurano said what happened in Kohala was not an isolated incident.

"Events like these are much more common than we'd like. Looking at brown waters in areas like West Kauai, South Molokai and many other areas after rain events is evidence enough that water pollution from land-based sources is a real problem and it's ongoing," he said.

In the Kohala case, Kurano noted that much of the landscape, at one time covered by native dryland forest, has been impacted by goats, past agricultural use, and recent residential development. He said the non-native grasses now covering much of the region are a poor barrier against runoff during heavy rains.

Although no one was penalized for directly contributing to the October 2006 sedimentation, the Clean Water Branch cited two property owners and the state Department of Transportation, which had road projects in the area, for violating state water pollution rules by failing to employ proper erosion-control measures.

The Clean Water Branch also worked with the Kohala Ranch Homeowners Association, where some of the construction was taking place, to adopt language in the group's rules requiring members to implement best management practices to mitigate potential pollution sources. In the meantime, the DOT improved culverts in the area and Hawaii County grading inspectors are paying more attention to construction activity along the Kohala Coast, Kurano said.

Walsh reports that 18 months after the flooding, little of the sediment had left the reefs. "It looked like it just happened," he said. There also were signs of coral bleaching and other "stress reactions."

Today, lower sections of the vertically growing reef are dead. "You go higher up and there is still a substantial amount of live coral. But the bottom on all these reefs is dead, and if the coral is dead, it loses its ability to resist erosion," Walsh said. "In the long run if we don't get coral colonization, the higher sections will be undermined."

Whether the sedimentation will cause more far-reaching damage is uncertain.

"We don't really know what long-term impacts are. One thing we're finding at several study sites in northern zone (adjacent to the sedimentation) is that over a period of the last eight years we've noted double-digit declines in live coral cover ranging up to 20 percent," Walsh said. "Whether this event contributed to that in some way, we don't know. Something is happening."

Reach Christie Wilson at cwilson@honoluluadvertiser.com.