One of California’s foremost experts on freshwater fish believes there may be hope for restoring native salmon to abundance – but there’s a catch: California must build the controversial Delta tunnels, he says.

“The expected costs are tremendous and there is a lot of concern over that, but our paper is about what’s good for fish,” said Peter Moyle, a professor of fisheries with the University of California, Davis Center for Watershed Sciences. “Will the Delta tunnels be good for fish or not? I think they will.”

Moyle co-authored a 63-page report with colleagues John Durand and Carson Jeffres that was released on Tuesday. It proposes a comprehensive game plan for restoring the Sacramento-San Joaquin Delta and saving native fish from extinction. Achieving this goal, according to the report, will require restoring a great deal of riverside habitat in the northern and western Delta. Saving the native fish, the report says, will also probably require building the Delta tunnels, or something resembling them.

The tunnels, known officially as California WaterFix, would create a new conveyance system under the delta at an estimated cost of $17 billion. Such an alternative water diversion system, the authors explain in their paper, could help alleviate strains on the Delta currently caused by powerful water pumps at the south edge of the estuary, as long it is coupled with large-scale habitat restoration projects.

The paper was commissioned by Orange County Coastkeeper, which received guidance and direction in the effort by the Municipal Water District (MWD) of Orange County, according to meeting reports from late 2016 and early 2017. Garry Brown, the executive director of Orange County Coastkeeper, said his organization funded the paper and that no funding came from water agencies.

But Barbara Barrigan-Parrilla, executive director of the group Restore the Delta, which opposes the tunnel project, believes the paper’s findings were influenced by the MWD. The district receives water from the Delta via the State Water Project and potentially has much to gain from the tunnels, which its supporters say will improve the consistency and reliability of deliveries.

“I believe Dr. Moyle delivered a theory based on the opinions of the people who funded his work,” Barrigan-Parrilla said. “It’s really heartbreaking. [Peter Moyle] is going to wind up on the wrong side of history.”

Moyle said that for him “What matters is being on the right side of protecting native fishes. Critics need to come up with a comprehensive, realistic plan for fish conservation that takes into account major changes to the delta that are likely to happen in the not-too-distant future.”

The new report comes at a time when the Delta smelt is nearer to extinction than it has ever been and when Chinook salmon numbers have plunged following years of drought-related stress. In fact, Moyle co-authored a report just 10 months ago predicting that most of California’s native salmon and trout would vanish over the next few decades.

“We predicted they’d go extinct if present trends continue,” he said. “The new report is a plan to make present trends not continue.”

The paper – entitled “Making the Delta a Better Place for Native Fishes” – aims to provide lawmakers and policy directors with a framework to reverse the trends that have made the Delta such a hostile place for native fish that evolved to thrive in an estuary environment.

After decades of aggressive water diversions, much of the Delta now functions ecologically more like a Mississippi basin swamp than like an estuary. One key feature of an estuary is that freshwater flows relatively consistently through the system, toward the sea. That flow pattern has been disrupted in much of the Sacramento-San Joaquin Delta, Moyle explained.

“We have an ecosystem in most of the central and south Delta that just isn’t suitable for most of the native fishes we want to have around,” he said.

Currently, two large pumping stations at the south edge of the Delta draw water into a pair of canals taking the water south and west. The pumps, run by the United States Bureau of Reclamation and the California Department of Water Resources, are so powerful that they actually reverse the flow of the Sacramento and San Joaquin rivers at times, confusing migrating fish and drawing them toward remote backwaters and the pumps themselves. This phenomenon has killed many millions of salmon, smelt and other native species over several decades.

The new report outlines a state-mandated project called EcoRestore, initially introduced several years ago as a mitigation to the Delta tunnels project. EcoRestore would protect or revive about 30,000 acres in the Delta region – mainly floodplain and inter-tidal habitat. The report’s authors suggest expanding this project while focusing restoration efforts on a region of the estuary sometimes called the “North Delta Habitat Arc.” This area begins in the Yolo Bypass floodplain region southwest of Sacramento and extends south and west along the course of the Sacramento River. It has been spared some of the most drastic impacts and landscape alterations seen in the south Delta and to biologists is a key area of focus for habitat restoration projects.

“This is where the best opportunities are for habitat restoration, and the best place to spend money for restoration,” Moyle said.

The paper doesn’t exactly introduce any new concepts in Delta restoration. What it does do, Moyle said, is present the needs of the Delta in one cohesive document.

“People know what the fish need,” he said. “It’s more a matter of connecting all the dots to make a coherent restoration program.”

Where the report is likely to fire up debate and criticism is its discussion of the hotly contested Delta tunnels. The project’s detractors have long warned the tunnels could easily lead to increased volumes of water being removed from the Delta – which they say could push salmon and other species over the brink.

“If they build it, salmon will do worse than they are now, and we’ll lose Delta smelt,” Barrigan-Parrilla said.

Moyle acknowledged there are risks associated with building and operating the tunnels, but it’s still a project he stands behind. Moyle said he feels the objections to WaterFix are misguided – at least as far as rebuilding salmon runs is concerned.

“The status quo is not sustainable; it will result in the likely collapse of many remaining stocks of desirable fishes even with large investment in restoration projects,” the new report warns, referring to the existing water diversion system.

Moyle and his co-authors make the case that a pair of tunnels could alleviate the reverse-flow problem by diverting water from the north end of the estuary. This water would be moved underground and would connect to the existing conveyance system. The south Delta pumps would be throttled back, or even shut down for much of the year, and the end effect would be an uninterrupted seaward flow of water – exactly what could restore the Delta to health.

“But there are a lot of ifs, buts and ands here,” Moyle said.

For one thing, huge fish screens must be installed in front of the tunnel intakes to prevent increased mortality of salmon – barriers that the report cautions might not be effective. The report also cautions that the tunnels will only benefit fish populations if all possible mitigations, including floodplain habitat restoration, are completed. Moreover, the authors warn that, once the tunnels are built, total water exports must not increase.

That’s what John McManus worries will happen. The executive director of the Golden Gate Salmon Association, a fishery advocacy group, McManus agrees with Moyle that the existing water diversion system threatens to annihilate Central Valley Chinook. However, he says the huge size of the proposed tunnels is reason to believe they will be used to take unsustainable volumes of water from the Sacramento River.

McManus added that a single-tunnel version of the project – now being considered by the state – could also be harmful to fish. Moyle’s report assessed a single-tunnel alternative but decided it would be little better than the status quo “because it lacks flexibility” and would mean running the Delta pumps at relatively high rates.

The research community seems generally skeptical of the capacity for the proposed tunnels to benefit fish. A study published in February by the U.S. Geological Survey concluded that the project would likely increase negative impacts on juvenile Chinook salmon. Rene Henery, California science director for the group Trout Unlimited, feels Moyle has endorsed the tunnels because he considers the better alternative – reducing overall water exports – politically unfeasible.

“But so many things, until they happen, are politically unfeasible,” Henery said. He added that “forcing an infrastructure project that is so controversial” could widen society’s political fissures and make progress in environmental restoration an even more arduous task than it already is.

Brown, at Orange County Coastkeeper, said his group does not necessarily support the tunnels.

“But I think it’s okay to have a discussion about them,” he said. “Some people have become so committed to the fight against California WaterFix that they will overlook the finer points in the paper about habitat.”

Moyle says saving fish species was just one reason he wrote the report. He also was eager to help bridge a significant political gap between Northern and Southern Californians. Decades ago, Delta water was exported primarily for use by San Joaquin Valley farmers and cities in Southern California. Today, millions of people in the Bay Area use the Delta’s water, too.

“The idea is to present this as a common problem,” Moyle said. “We all get water from the Delta now, so it’s a statewide problem. It’s everyone’s problem.”