It stands less than an inch tall, sports a cinnamon belly, munches on pickleweed and spends its nights dodging owls and raptors in the Palo Alto Baylands.

Now, this tiny critter threatens to delay a $16.7 million, regional flood-control plan that took years to formulate and that aims to protect Palo Alto, East Palo Alto and Menlo Park from the dreaded 100-year flood.

Behold the salt marsh harvest mouse.

The mouse weighs only about 20 grams, but its tiny frame is casting a large shadow over the environmental-review process for the flood-control project, which has already received the blessings of all three cities. As an endangered species, it is protected by reams of state and federal regulations, including ones overseen by the U.S. Fish and Wildlife Service. These days, as Fish and Wildlife considers granting a permit to the San Francisquito Creek Joint Powers Authority for the flood-control project, the safety of the tiny, tawny mouse has become a big concern.

Last month, Fish and Wildlife indicated in a letter to the U.S. Army Corps of Engineers -- the agency coordinating the project on the federal level -- that the environmental analysis conducted so far doesn't fully satisfy its concerns about endangered species. Fish and Wildlife is particularly focused on the Faber Tract and the adjacent Laumeister Tract in East Palo Alto, large swaths of marshland in the northwestern portion of the Palo Alto Baylands that is a home to dozens of California clapper rails, an endangered bird, and that boasts "an important population of the salt marsh harvest mouse," according to Fish and Wildlife.

The environmental agency, which is part of the U.S. Department of the Interior, took issue with the alternative chosen by the San Francisquito Creek Joint Powers Authority, which would widen channels by reconstructing levees in the downstream area, including at the Palo Alto Municipal Golf Course. Another alternative that the creek authority evaluated during the environmental review was creating a new bypass channel on the golf course for flood water.

Fish and Wildlife argue that the selected alternative, by pushing water to the Faber Tract during floods, reduces the land clapper rails and harvest mice would have for escaping predators. It also takes issue with the assertion that the flood-control project "is not likely to adversely affect the California clapper rail and salt marsh harvest mouse."

"Since most predation on California clapper rails and salt marsh harvest mice occur during flood events, the Service believes that the proposed increases in the frequency, duration and height of flood flows within the Faber Tract and loss of availability of upland refugia cover will result in a significant increase in the rates of predation," Fish and Wildlife stated in the July 3 letter.

The project, the agency argues, "has the potential to have severe adverse effects to the California clapper rail and salt marsh harvest mouse."

"The Service believes that the Corps and JPA should implement other alternatives to reduce flood risk in San Francisquito Creek such as passing flood flows through the Palo Alto Municipal Golf Course ... rather than through the Faber Tract."

If the creek authority chooses to proceed with the project as designed, it would have to include more than a dozen mitigations, including a new "upland refugia" for the rail and the mouse. This could mean installation of "marsh mounds" for the two species near or within the Faber and Laumeiser tracts. The creek authority was also directed by Fish and Wildlife to regularly monitor rodent traps to ensure that no salt marsh harvest mice were captured and to report any instances of captured harvest mice to the agency.

Len Materman, executive director of the creek authority (an agency that includes elected officials from the three cities, as well as from the Santa Clara Valley Water District and the San Mateo Flood Control District), said the group is in ongoing negotiations with Fish and Wildlife about the proposed mitigations. The creek authority, he noted, already thoroughly studied the golf-course alternative during its environmental review, and officials concluded that it would cause "significantly greater" harm than with the channel-widening option.

Materman told the Weekly the agency doesn't expect the concerns from Fish and Wildlife to ultimately delay the project. However, the criticisms have already prompted the creek authority to change the sequence of its work. The authority applied for the permits in March and was hoping to have them in place in time to start in-channel work in early September. That now seems highly unlikely. And given that the agency isn't allowed to work in the creek after mid-October because of the presence of steelhead trout, in-channel work will now have to be deferred until next year, Materman said.

At the same time, Materman said, the agency is confident that it will get the permits without delays to the overall project. Some of the mitigations proposed by Fish and Wildlife are already part of the project, while others will be integrated into the design. These include the marsh mounds. The creek authority, he said, has been working with Fish and Wildlife and with the Bay Conservation and Development Commission to determine the locations and designs of the mounds.

"We are looking to incorporate new mounds into the design of the project to address that concern," Materman said.

With the channel off limits because of permitting complications, the agency has been focusing on other elements of the project, including work with PG&E on alterations to electric lines crossing the creek and with the East Palo Alto Sanitary District to deal with a sewer line crossing the creek.

"What we're really focused on now is: What kind of things can we do outside the channel so that we can get these things out of the way?" Materman said.