The California Water Commission’s February meeting included a brief presentation by Dr. Lenny Grimaldo, Environmental Director for the State Water Project, on the project’s recently issued Incidental Take Permit (ITP). This updated permit, approved by the Department of Fish and Wildlife in October 2024, is critical in regulating activities that could affect species protected under the California Endangered Species Act (CESA).
The 2024 ITP includes provisions for Delta smelt, longfin smelt, and both winter-run and spring-run Chinook salmon. Additionally, the permit extends to white sturgeon, a species currently under consideration for listing by the Fish and Game Commission. While the listing decision is pending, specific measures are required to ensure its protection.
This updated permit represents a significant shift in approach for the state. Prior to 2020, California relied on federal permits, achieving compliance through a consistency determination with federal guidelines. However, in 2020, diverging priorities between state and federal agencies led California to seek an independent permit to address species covered by CESA. Notably, all the species included, except white sturgeon, are also federally listed.
The permitting process extended into 2024 and involved three years of complex negotiations with state and federal agencies. Despite the challenges, the outcome is seen as a significant achievement. Dr. Grimaldo described the result as “a new set of rules” that balances environmental protection with water supply needs. By incorporating the latest scientific developments and technological advancements, the permit ensures the continued safeguarding of critical species while supporting water reliability for the state.
Delta export operations are driven by whether or not fish are present and at risk from entrainment by the pumps, and the new rules are responsive to those factors.
Another key measure is spring outflow, which reduces exports to allow for outflow to San Francisco Bay to enhance rearing habitat for longfin smelt and other species.
The graphic on the left is meant to illustrate spring outflow. The top figure shows a dry year with low flows. The blue to green colors are the low salinity habitat that endangered species rely on. “If you take a snapshot from the Golden Gate to the Delta when it’s very dry, that low salinity habitat that a lot of our endangered species rely on is very compressed to the Delta,” said Dr. Grimaldo. “If you look at the figure on the bottom, that’s under high outflow, and you see those color bands expand all the way from the Delta to San Francisco Bay. So, under high flow, you have more habitat. This is really important for these well-documented relationships between outflow and abundance.”
The chart shows the effect of the new rules, with the dark blue being the 2024 ITP and the green being the 2020 ITP.
“The climate is very different now,” said Dr. Grimaldo. “We get less snowpack, so we really need to design rules on trying to capture water when it’s moving down and rely less on snowpack. So the rules are designed to be more flexible under those conditions, and that’s a good thing for fish, too, because those are periods when we have a lot of outflow; they actually move right past the pumps. But we also have a lot of analyses that suggest when it’s too turbid, we need to dial back. But for the most part, we looked at updated science to inform how those rules would be developed.”
The punch line is, during these wetter periods, the State Water Project is capturing more water, and this doesn’t even include adaptive management, which may increase the flexibility down the road.
Dr. Grimaldo gave an example of how the permit has already saved about 12,000 acre-feet of water that would have otherwise been lost. “In the past, when we saw salmon at the pumps, we would look at a size chart and say, Okay, that’s four inches long. That’s probably a spring run. We’re not sure, but we’re going to curtail the pumps. In 2020, that was the technology we had. But now we have this new technology called our Sherlock program within DWR where, within an hour, we can get the genetic confirmation of whether it’s a protected run or a nonlisted run. Then, our exports are modified per the outcome of the genetic test that we get in real-time. So this is an example of a new rule that’s generating already improved water supply for the state.”
The state has been making significant investments in science and monitoring that are now coming into play, such as real-time monitoring and enhanced fish-tagging technologies. Another investment paying off is the Georgianna Slough Migration Barrier, which has been estimated to keep 85% of salmon in the Sacramento River instead of the interior Delta and toward the pumps.
Dr. Grimaldo said the best part of the ITP is the adaptive management program. DWR and DFW worked hard to design an adaptive management process that allows for making real-time decisions.
“These are wicked problems because it’s not a lab situation – you can’t control what fish or where in any given year or how much flow is coming down,” he said. “That always changes. So you have to be able to take in information and address it in a way that allows some performance metrics … do we need to do the action differently based on this information, or do we continue as is? So for us, using adaptive management will be critical for the Department over the next 10 years of implementation to continue to improve how we manage the projects to benefit water supply and protect fish.”
Commissioner Sandi Matsumoto asked if any adaptive management decisions would be used to improve conditions for fish.
Dr. Grimaldo said an ultimate outcome of the Wanger court decision many years ago was the development of life cycle models for the Delta smelt. “So for us, adaptive management includes looking at these life cycle models and different predictions, such as will this habitat really increase the population? Maybe it won’t, taking that uncertainty and designing a science program around that to collect information for whatever action we do. If we don’t do an action, or maybe we do a modified action or a full action, we need to learn as we go along. So in that way, it’s using the life cycle model and advanced statistics to help generate predicted outcomes that we can test and then learn from that.”
Commissioner Matsumoto acknowledged the examples given are real-time operational decisions, but what about the trends of the fish species?
Dr. Grimaldo acknowledged that many fish species have been declining over time, although he pointed out that longfin smelt this past year had the highest abundance since 1985, the third highest since 1990, and it was the year class coming off a drought year. “Something happened that wasn’t related to flow. It was food or habitat where we’re restoring habitat. We need to look at that because there was a major rebound in longfin this past fall that’s not explained by simple math.”
I would argue that climate change is having a bigger impact on the trends over time because we solved the entrainment program problem, for the most part,” he continued. “A lot of our rules are prescriptive now. They rely less on real-time assessments because we know how fish will respond. We’ve been doing this for a long time and analyzed a lot of data. We’ve been looking at the trends, and the number of fish we collect at the pumps has gone down over time, but so have species trends, and water temperature, invasive species, and other factors are not helping, and sometimes they’re not identified.
“It’s easy to look at the projects and say they’re the problem, but for us, it’s not a one-dimensional problem with the projects; it’s a three-dimensional problem,” he continued. What I believe is that in looking at the data, the percent of the variability explained in a species trend – the State Water Project has not contributed further to that decline. It’s been holding constant over time, which means other factors are driving these species trends.”
