California’s ambitious plan to tunnel under the West’s largest estuary has always had two primary goals: to restore imperiled native fish and to improve water deliveries to farms and cities. An early analysis by federal wildlife agencies, however, indicates the project might make life worse for fish.

The so-called WaterFix project calls for building two giant tunnels under the Sacramento-San Joaquin Delta, a tidal estuary that nurtures the largest salmon run on the West Coast. The tunnels, each 40ft (12m) in diameter and 35 miles (56km) long, would shunt a portion of Sacramento River flows out of the estuary and directly to existing water distribution canals south of the Delta, near the city of Tracy.

Some 25 million Californians rely on the Delta for at least a portion of their water needs. The diverted water also irrigates more than 3 million acres (1.2 million hectares) of farmland. But this water supply has become less reliable in recent years amid pumping reductions to protect native fish, including Chinook salmon, delta smelt, steelhead trout and sturgeon.

The tunnels, estimated to cost $17 billion, are intended to bring reliability back to the water diversions. This would be done by moving the diversion point north, to a presumably less sensitive location on the banks of the Sacramento River, with improvements like modern fish screens and 15,000 acres (6,070 hectares) of habitat restoration.

But big water projects come with big conflicts. And despite 10 years of work on the proposal, it may still present significant risks to fish.

The U.S. Fish and Wildlife Service and National Marine Fisheries Service recently released draft studies detailing how the tunnel project might affect fish protected by the Endangered Species Act. Known as a “biological opinion,” each agency’s report is still undergoing extensive internal review and fine-tuning.

Even so, the drafts identify problems that may be difficult to overcome, or which might require extensive modification of the tunnel project.

“It’s obvious there will be adverse effects from this project,” said Holly Doremus, a professor of environmental law at U.C. Berkeley and an expert on the Endangered Species Act. “These fish are in a bad way. There’s a desire to have higher reliability for high volumes of water delivery. That isn’t compatible with certainty that the fish will be in better shape.”

The draft biological opinions are even more significant because key sections have already been reviewed by an independent science panel assembled by the Delta Stewardship Council, a state agency.

Significantly, the panel found that 15,000 acres of habitat restoration won’t be enough to neutralize damages caused by the project.

“Adverse effects of construction and operation will require significant mitigation beyond the conservation measures described,” the six-member panel of experts wrote in its report, completed in March.

A spokesperson for the WaterFix project did not respond to a request for comment.

Concerns identified by federal wildlife officials include:

• Delta smelt could be cut off from habitat upstream of the three tunnel intakes on the Sacramento River during the 10-year construction period. Construction will narrow the river, boosting water velocity beyond what smelt can handle.
• Once operational, water diverted by the new intakes will cause salinity to shift upstream in the estuary. This could further constrict smelt habitat.
• The suction effect of the intakes could cause reverse flows both upstream and downstream that could be harmful for salmon and smelt.
• The project includes changing how upstream reservoirs release water. This could increase water temperatures and shrink spawning habitat in the Sacramento and American rivers, which would be deadly to salmon.

In its draft biological opinion, the National Marine Fisheries Service writes that tunnel operations could kill as much as 7 percent of winter-run Chinook salmon, an endangered species.

“This is a notable survival reduction for an endangered species, especially if it occurs on a frequent (e.g., annual) basis,” the report notes.

Federal officials emphasized that their review of the complicated project is ongoing, and any findings in the draft biological opinions could change.

“The WaterFix proposal is not entirely ripe for final consultation,” said Shane Hunt, a spokesman for the U.S. Fish and Wildlife Service. “They have proposed some minor adjustments. So until they put pens down on tweaking what they’re proposing to do, we won’t have a final biological opinion.”

State officials hope to have all permits for the project in hand by the end of this year, with groundbreaking to start in 2018.

Hunt emphasized that a final biological opinion, in fact, will not be the final word on managing the project’s environmental effects. That’s because some aspects of project operations will be decided later, after construction has begun. As a result, the wildlife agencies will continue to watchdog the project and may impose additional limits on certain aspects of tunnel operations.

But that’s particularly worrisome for Delta smelt, said Doug Obegi, an attorney with the Natural Resources Defense Council. The fingerling smelt, a threatened species, is widely considered an indicator for the overall health of the estuary.

“The species is nearing extinction, and continued loss of habitat under the proposed action significantly threatens the ability of a self-sustaining delta smelt population to persist,” Obegi said. “You can’t, in the Endangered Species Act context, approve a project assuming the problems will magically get fixed in the future. It actually is worse than the status quo.”

A key question is whether the final biological opinions will reach a so-called “jeopardy” conclusion. In the context of the Endangered Species Act, this means operation of the project is likely to jeopardize survival of a protected species.

If that were to happen, the agencies would work with the state to develop an alternative known as “reasonable and prudent actions.” This could include a wide variety of modifications, such as shrinking the size of the project or restricting how much water it can divert.

The prospect of less water could unbalance the already difficult financing for the expensive project. It could also, Doremus said, lead to political meddling to weaken wildlife protections. That’s not far-fetched at a time when both the president and Congress are pressing to weaken the Endangered Species Act.

“You can imagine the political context of a situation like that … and the pressure that would put on Congress to allow it to go ahead,” she said. “It’s not hard to imagine that a jeopardy finding could be followed by a legislative exemption.”

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