When thinking of the potential impacts of the change, it is important to recognize that the WaterFix is not just a proposal for new conveyance facilities, it is a proposal for new operating rules that add significant new restrictions on the operation of existing pumps in the south Delta.
Since a phased approach is the same WaterFix project according to the state, all the WaterFix operating restrictions on the south Delta pumps would presumably still apply, even though the ability to divert from the north Delta would be lower during the single-tunnel phase. Those rules are part of the project, and I doubt they could be adjusted without creating a major setback in the permitting process. It is not clear that lighter pumping restrictions could be justified anyway because one tunnel could be just as bad for fish.
I have been told two reasons why one tunnel could be as harmful to fish as two tunnels even if it diverts less water from the Sacramento River. First, the smaller tunnel capacity would mainly reduce exports during high-flow periods when diversions are least damaging to the environment. Second, when lower amounts are diverted during lower-flow periods, fewer intakes would cause more concentrated, higher-velocity diversion rather than being spread over 3 intakes and 5-6 miles of river. So the main effect of one tunnel is to cut in half the capacity to divert water during high-flows, which has been touted as the main benefit of the tunnels.
So how much less water would be exported compared to two-tunnels? A scenario like this was modeled for BDCP "Alternatives to Take" analysis in 2013, and it found that compared to the proposed 9000 cfs twin tunnels; Delta exports would be 218,000 af lower with 6000 cfs conveyance and 517,000 af lower with 3000 cfs conveyance. This suggests a 4500 cfs one-tunnel WaterFix would reduce water exports in an average year by about 400,000 af compared to the twin-tunnel proposal.
Considering that the current 9000 cfs WaterFix only increases water exports by 200,000 af compared to No Action, that means one-tunnel WaterFix export about 200,000 af less than the No Action Alternative. The other benefits to water agencies, water quality improvements and seismic protection, would also be lower with one tunnel.
Finally, CVP contractors aren't participating in the WaterFix, and have been assured their south Delta diversions will not be harmed by WaterFix. That could be hard to do in practice since the WaterFix permits depend on constraints to south Delta pumping, but it seems that the SWP would probably bear all of the costs of pumping constraints that were part of the WaterFix proposal. If endangered and threatened Delta fish continue to do poorly, CVP contractors will be arguing that this is due to WaterFix - not their south Delta diversion - and they will find plenty in the WaterFix EIR to support their position. The WaterFix could be blamed in the same way largemouth bass and water treatment plants are today.
Considering the reduction in benefits from a phased WaterFix and the prospect of new conflicts and more uncertainty, some water agencies that support WaterFix might want to reconsider their funding commitments under this phased approach.
As Michael Hiltzik with the LA Times wrote this fall, this is likely just another stumble as WaterFix "staggers to its deathbed."