An ambitious plan to reduce flood risks for Palo Alto and Menlo Park residents near the Pope-Chaucer bridge is now on the verge of faltering after the agency overseeing the project concluded that the long-awaited replacement would actually endanger downstream areas.

The analysis, which was released this week and which the San Francisquito Creek Joint Power Authority board of directors discussed at a special meeting Thursday, represents a stinging setback for the agency's plans in what's known as "Reach 2" — the area between Newell Road and Pope Chaucer bridges. The creek authority had been planning to replace the Newell Road bridge and to widen the channel before commencing work on the Pope-Chaucer.

While the first two components of this plan remain on track, the new analysis from creek authority engineer Jack Xu is forcing the agency to reconsider its plans for the Pope-Chaucer bridge. The analysis concluded that unless the three cities along the creek — Palo Alto, East Palo Alto and Menlo Park — install flood walls along much of the creek, the risk to downstream areas such as University, Woodland and Euclid avenues would become significantly greater as a result of the Pope-Chaucer replacement. That's because in its current configuration, the flood-prone bridge functions as a dam during storms, restricting flow to downstream areas.

"If Pope-Chaucer is in place, the communities on University and downstream will never see a flow higher than a certain amount," Xu said. "When you remove that bridge, suddenly all the water gushes down and you'd have to protect those people from all the water that would come down if you remove the Pope-Chaucer."

The agency began to revisit its assumptions about the hydrology of the volatile creek after the New Year's Eve storm, which caused flooding near Pope-Chaucer and in other sections around the creek. Xu said the flooding during that event did not match what the creek authority's modeling had predicted. The existing model, which was based on a 2009 analysis by a consultant, relied on data from four prior storms, all of which were less severe than the one that occurred during New Year's Eve.

Xu's report notes that the prior model had underestimated the "roughness" of the creek — a measure of vegetation, debris and other blockages that interfere with the creek's flow. The prior analysis had also overestimated the capacity of the channel by as much as 2 feet in some area, the report states.

To protect downstream communities from increasing flood risk resulting from the Pope-Chaucer bridge's removal, the creek authority would have to build flood walls 1,000 feet in length and 1 or 2 feet in height, depending on the level of protection that the agency would be seeking to achieve.

Given the findings, the creek authority is preparing to reopen some of the other flood-control alternatives that it had evaluated in the Environmental Impact Review for the "Reach 2" section of its plan. This will include, among other things, further evaluation of options for detention basins upstream.

Tess Byler, project engineer at the creek authority, said the recent analysis made it clear that the hydraulics at the creek have changed.

"That's a shock to everybody," Byler said.

Both she and Xu suggested that moving ahead with the Pope-Chaucer removal would be politically difficult, given historical opposition by property owners along the creek to having floodwalls installed along the creek.

"It would be very difficult to get a project where you can remove Pope-Chaucer," Xu said. "It would take a lot of floodwalls. The history of the project shows there's no appetite for that."

The news also came as a shock to the residents in Crescent Park in Palo Alto and the Willows in Menlo Park, many of whom have been lobbying for the Pope-Chaucer bridge to be replaced since the major flood of 1998. Tom Rindfleisch, a Crescent Park resident who has been tracking the ebbs and flows of the flood-control project for years, said Thursday that many people in his neighborhood have trouble sleeping during rainy seasons because of flood risks. He challenged the creek authority not to abandon the project.

"There are going to be people who are really put out by this because of the continuing fear over the winter rain season on how they can protect their homes and their lives and their properties," Rindfleisch said. "I believe the solution has to be get rid of Pope-Chaucer bridge and fix the downstream creek so it can hold the capacity for what will undoubtedly flow downstream."

Menlo Park City Council member Drew Combs, who chairs the creek authority's board of directors, shared his disappointment. Months ago, he had been telling residents in flood-prone areas near the creek that the long-delayed project would be finally coming, Combs said. He had also believed that the construction on Reach 2 would start before his term on the creek authority expires, a prospect that now seems less likely.

"This is a general frustration with the situation, but facts are facts. The science is the science," Combs said.

Palo Alto Vice Mayor Greer Stone, who also serves on the board, urged the creek authority's staff to consider possible mitigations that could improve flood control in case Pope-Chaucer is not replaced. He called the new analysis "concerning."

"Some of the residents impacted by flooding there finally saw light at the end of the tunnel for that portion of the creek," he said.

Given the latest findings, the creek authority plans to take a fresh look at other design alternatives, a process that will likely require additional analysis and will almost certainly delay the project even further. Board member Rebecca Eisenberg, who represents the Santa Clara Valley Water District on the creek authority's board, urged staff to explore emerging technologies and other mitigation strategies to address flood control.

"Because the current situation is not tenable… It's just not," Eisenberg said. "The answer can't be, 'So sad. Too bad. Live with it.' That's not going to be OK."

A new analysis by the San Francisquito Creek Joint Powers Authority has found that replacement of the Pope-Chaucer would send more water downstream, putting that area at risk of flooding.