An effort by Palo Alto, East Palo Alto and Menlo Park to improve flood protection around the volatile San Francisquito Creek earned a hard-fought victory on Friday afternoon, when officials learned that the project is on the verge of earning a permit from a state agency that has been withholding it for more than a year.

The determination by the Bay Area Regional Water Quality Control Board was announced at a special meeting at Stanford University, which brought together top staff from the water board and the San Francisquito Creek Joint Powers Authority, the agency that is spearheading the $37 million flood-control project.

Though the project still has to receive the approval from several federal regulatory agencies, most notably the Fish and Wildlife Service and National Marine Fisheries Service, the certificate from the water board removes what so far has been the steepest obstacle for the project, and clears the way for other agencies to issue their own permits.

The project includes rebuilding and modifying levees near the Palo Alto Golf Course, installing new flood walls, and removing sediment from the creek channel to improve water flow. The project aims to protect the particularly vulnerable areas downstream of the creek, between Highway 101 and the San Francisco Bay, including a portion of East Palo Alto and Palo Alto's Crescent Park neighborhood.

If the water board issues the certificate in the next week, as the board's Executive Officer Bruce Wolfe assured the three cities Friday, it will end a process that was launched in March 2013 and continuously surprised, frustrated and angered council members and residents from the affected cities.

In March of this year, after months of negotiations and repeated requests for new information and further analysis, the water board rejected without prejudice the application for the flood-control project. Officials from the three cities have long maintained that many of the requests fall far beyond the scope of the water agency, and that the water board's actions are endangering the lives and property of thousands of residents who live near the creek.

The creek authority made some design modifications in response to the water board, including a raising of the flood walls to protect the Faber Tract from flood runoff, and submitted a new application on July 31.

Dozens of East Palo Alto residents, including those whose homes suffered massive flood damage in the February 1998 flood, made a trip to Oakland in August to make their case for the project to the regional water board. At that meeting, the board of directors of the state agency agreed that the project should move forward as soon as possible, and affirmed that the decision to issue the certificate would be made by Wolfe rather than by the board.

Two weeks after that meeting, Wolfe issued another letter finding the latest application incomplete and requesting more information. The board's August letter brought up dozens of new questions and demanded more information, including details about monitoring methods, flood wall designs, and assurance that the proposed levee would not provide inferior protection to East Palo Alto than to Palo Alto, as some critics have maintained.

It also proposed splitting the project into two phases, with the bulk of the work on the East Palo Alto side taking priority, a suggestion that the creek authority deemed as infeasible because it would substantially change the project and require the agency to redo much of its work.

On Friday, Wolfe acknowledged that while some of the questions in the August letter of incompletion pertained to issues that needed to be resolved for certification, others were there mainly to help the water board answer questions from the public. He said five different staff members worked on putting together the letter and explained that this is why it seems like it was written "by committee."

Most importantly, Wolfe made it clear Friday that he now has all the information he needs to give the creek authority the certification it has long been seeking. The certification would be issued as soon as the U.S. Army Corps of Engineers releases its officials public description, which is expected to happen in the coming weeks.

The built-up tension between the water board and the creek authority was on full display at the Friday meeting, with top staff from the two agencies offering their own histories of the project and explanations for the delays. Water board staff also fielded repeated accusations from local officials about the lack of transparency in the process, with Palo Alto City Manager James Keene and creek authority Executive Director Len Materman taking the lead.

Materman and Kevin Murray, project manager at the creek authority, argued that the entire process was marred by secret meetings between the water board, project opponents and other regulatory agencies – meetings from which the creek authority was explicitly barred. This, they maintained, led to great confusion, unacceptable delays and unexpected denials and requests. In many cases, previously answered questions and analyzed design options re-emerge time and time again as obstacles to approval. This included proposals to use more land from the Palo Alto Municipal Golf Course and Palo Alto Airport for the flood-control project.

Greg Stepanicich, attorney for the creek authority, argued that the water board's denial of the application should never have occurred. If the water board had concerns, it should have raised them and the creek authority would deal with them, Stepanicich said.

Wolfe had explained that the denial was dictated largely by the calendar and board's determination that the permit could not be granted within the required one-year timeframe. But both Stepanicich and Materman maintained that the surprising denial in March prompted all the other federal regulatory agencies to halt their work on the project, significantly setting the project back. The delay, Stepanicich said, "should not have occurred."

"Simply, it makes no sense to us when the denial comes out of the blue," Stepanicich said. "It changed the whole ballgame here when we had a denied application. That is what disrupted the process with the federal agencies."

Wolfe disagreed and maintained that because of "streamlining requirements," the water board had 30 days to respond to the city and because it determined that it could not issue its ruling within this time frame, he felt denying the application is the best way to keep the process moving along.

"I stand by that action," Wolfe said.

After Wolfe declared that he now has everything he needs to deem the application complete, Stepanicich asked if he can have a letter putting that in writing in the next week. Wolfe agreed.

The U.S. Army Corps had also indicated last month that it deems the creek authority's recent application to the Corps to be complete, Wolfe said. Once the Corps issues its official description of the project, which it is expected to do in the next two weeks, the certification from the state board would be issued.

Wolfe said the water board's concerns about protecting the endangered species -- clapper rail and salt marsh harvest mouse -- in the Faber Tract have been "largely resolved," not 100 percent but "close enough that we can move forward." He noted, however, that the National Marine and Fisheries Service has indicated that it has its own concerns about protecting species in the upper portion of the creek channel and that it could take months to resolve those issues.

The meeting included three board members from the water board, including board Chair Terry Young, who led the meeting and reminded the public that "we're not here to talk about the past" but to "get through to the future." Board members Newsha Ajami and Margaret Abe-Koga, a Mountain View councilwoman, also participated in the roundtable meeting at Stanford's Spilker Engineering & Applied Sciences Building. Representing the creek authority's board of directors were Palo Alto Councilman Pat Burt and East Palo Alto Councilman Ruben Abrica.

Both Burt and Abrica spoke about the re-emerging question of whether East Palo Alto and Palo Alto would get equal flood protection from the project. The levee on the Palo Alto side would be larger by a few inches because it would be a new structure and would need to settle, while the one on the East Palo Alto side is built on top of an existing levee, Burt explained.

He noted that the explanation has been offered time and time again over the past eight months but the question keeps returning, most recently in the August letter from the water board that asks whether the project is sufficient to protect the health and safety of the two communities. Burt noted that it would offer protection to the area from a 100-year flood, a goal that the communities have been pursuing for more than 15 years.

"The implication is that this is still a concern and it's still confusing, despite the amount of times that the settling of levees (question) has been asked and re-asked," Burt said. "I want to put that to rest."

Abrica agreed and said that recent back-door insinuations that East Palo Alto isn't getting as much protection as its neighbor is based on bad information and has "revived some very strong reactions in our community." East Palo Alto council members, he said, have been working with their partner cities for more than five years to finalize this project and they fully support it.

Wolfe said later in the meeting that he feels the issue of adequate protection for East Palo Alto "has been addressed" and called it a "local issue."

Keene focused on the "transparency issue" and urged that the "bias should be toward completion as opposed to delay." The water board should focus only on its own purview, he said, rather than anticipate the concerns of other agencies and delay its approval based on those concerns.

Materman made a similar point in his presentation.

"We believe the quickest way to complete all the permits is if each agency completes its permit," Materman said.