"Every tree that falls upstream winds up getting tangled up somewhere along this reach," he said. "It all contributes to the problem."

Vast quantities of submerged debris and other challenges have caused the ambitious effort by the Burlington County Bridge Commission to cost more and take longer than originally planned.

The creek, a tributary of the Delaware River that flows through Burlington County, unleashed severe floods in recent years that forced hundreds of people from their homes and left an estimated $25 million of property damage.

County officials projected two years ago that removing debris over nine miles of the creek in Southampton, Lumberton, and Medford would lead to healthier, freer-flowing waters and would potentially lessen the effect of future storms.

The commission has already spent or allocated more than the $2.5 million planned, records show, even as two of the creek's four targeted reaches are yet to be cleaned.

And the original end date of spring 2009 for the entire project - a target announced at an April 2008 news conference - was pushed to the end of the year on the current reach of the creek alone.

Commission Chairman John Comegno described the efforts as necessary and his agency's actions as fiscally prudent. Despite the unexpected challenges, he said, the commission has moved as quickly as possible and cleanup remains on schedule.

Noting the project's complexity, he said: "We've actually moved with great speed."

The agency collects just under $30 million a year in tolls from motorists who drive across the Delaware on the Burlington-Bristol and Tacony-Palmyra Bridges.

The commission maintains those spans and six smaller bridges in Burlington County. It also acts as the county's economic development authority, appropriating toll revenues and selling bonds to undertake projects on behalf of municipalities in the county.

A series of dams collapsed during a severe rainstorm in July 2004, causing such devastating floods that the county was declared a federal disaster area. Another major flood in April 2007 brought urgency to ongoing talks about cleaning the creek, where debris had piled up for decades and obstructed its flow.

But the problem was too extensive for local towns to address on their own, so the bridge commission partnered with the county and took the lead on the project.

The commission immediately directed the firm Garden State Engineering L.L.C., of Branchburg, to map and survey dozens of debris fields, prepare a work plan, and help secure the necessary state environmental permits.

The Department of Environmental Protection granted a "general permit" for the entire project, rather than individual permits for dozens of debris fields. This eased an otherwise arduous regulatory process at a time when the DEP's then-commissioner, Lisa Jackson, publicly stated her commitment to seeing the stream cleared and described it as a model project.

Based on the consultant's estimates, the commission awarded a contract in June 2008 capped at $454,070 to Nupump Corp., of Malaga. The firm was the low bidder for the job of removing debris from a 1.4-mile reach in Southampton and taking it to a staging area for transportation to the county landfill.

Yet two weeks after Nupump began pulling debris in late summer, GSE discovered that Nupump was already nearing the financial limit of its agreement and would need more money to complete the job, records show.

After doing preparatory work for a year and earning over $500,000 by the time Nupump was awarded the contract, GSE had not accounted for a substantial amount of submerged debris.

"Material that is below the stream is very hard to quantify. . . . As we cleaned it, other material floated up," said Richard Moody, the company's project engineer.

The bridge commission quickly processed paperwork that would double the value of the contract, and instructed Nupump to continue working, records show.