California Bay Delta

The California Bay-Delta is where the Sacramento and San Joaquin rivers meet as they flow out of the Sierra and Cascade mountains– spreading out into 1,160 square miles of islands, canals, and shallow waterways before flowing into the San Francisco Bay. Before it was diked, drained, and developed, the Delta was a vast wetland complex of low islands, shifting channels, woody debris accumulations, and tule marshes. Today, the Delta is a patchwork of largely agricultural islands separated by deep channels and protected by 1,100 miles of levees. It hosts farms, fisheries, water projects, recreational areas, and neighbors the State capitol of Sacramento. Geographically, it is the largest delta on the Pacific coast.

Why is this system important?

The Bay-Delta is a complex ecosystem made up of interconnected tributaries, rivers, bays, wetlands, marshes, floodplains, and islands. It contains areas of rich biodiversity, supporting hundreds of species of birds (migratory and resident), fish, and other plant and animal species. Endangered and threatened species include the delta smelt, Chinook salmon, and ridgway’s rail. The Delta and Suisun Bay/Marsh together cover about 1,300 square miles (land and water) spanning 6 counties, hold 400,600 acres of high quality farmland, and are home to more than 550,000 people. The Bay’s watershed covers over 45,600 square miles and drains 40 percent of California. The Bay’s surrounding lands are home to over 7.5 million residents. The Bay-Delta is the hub of the nation’s largest water delivery system. Two-thirds of the state’s population, about 27 million people, depends on the Delta watershed for some portion of their water supply, as do more than 3 million acres of irrigated farmland. Water from the California Bay-Delta provides a critical base for most of the State’s economic output of $2.2 trillion in 2015. In addition to water supply and agriculture, the Bay-Delta supports other industries including tourism and recreation, technology, entertainment, and fisheries.

What are major challenges?

The Bay-Delta is confronted with many challenges due to extreme habitat alterations and its central role in California’s water supply. Water diversions impair natural flow regimes, migratory cues, and water quality, and entrain fish into water delivery systems. More than a century ago, Delta residents began to build an intricate levee system to channel water and dry out land, which converted hundreds of thousands of acres of seasonally and tidally flooded wetlands into fertile agricultural fields.

As a result of continued land use change and urbanization, 95 percent of the historical tidal marsh in the Delta has been lost and has led to major declines in native species. Other Delta challenges include land subsidence, nutrients (which affect plankton communities and aquatic plants), toxins/pollutants (which affect species survival and human food safety), invasive and introduced species (which lead to competition with native species, predation, and habitat alteration), and a boom and bust hydrologic cycle of floods and prolonged droughts. The Delta and Bay are interconnected, and stressors affect the health of both.

Water management decisions have significant financial implications for the economic interests of the State, and by extension, represents one of the most politically charged subjects in California. Additional complications arise from the differences in governance and science organization between the Delta and the Bay, which have their own unique, but interrelated management needs. Each of these challenges will be compounded by climate change.

How is restoration and scientific research organized?

Hundreds of government, non-government, academic, and private institutions are involved with Bay-Delta research, restoration, and science management. Several interagency science groups organize new studies, review study plans and proposals, write scientific papers and reports, and promote collaboration, including the Interagency Ecological Program, San Francisco Estuary Partnership, San Francisco Estuary Institute, Collaborative Adaptive Management Team, Delta and Bay Regional Monitoring Programs, and the California Department of Fish and Wildlife’s (DFW) Watershed Restoration Grants Branch.

A host of State and federal government agencies play roles in Delta science or management, including the U.S. Geological Survey (USGS), U.S. Bureau of Reclamation, U.S. Fish and Wildlife Service (USFWS), DFW, California Department of Water Resources (DWR), and the State Water Resources Control Board. The Delta Stewardship Council, created as part of the 2009 Delta Reform Act, is the State agency charged with creating the Delta Plan, a blueprint for how to connect the many stakeholders to further achieve the coequal goals of a reliable water supply and a healthy ecosystem. The Delta Plan includes a recommendation for better organizing science, which led to the creation of the Delta Science Plan in 2013. The Council’s Delta Science Program is charged with developing scientific information and synthesizing the state of scientific knowledge on issues critical for managing the Bay-Delta system. That body of knowledge must be unbiased, relevant, authoritative, integrated across State and federal agencies, and communicated to Bay-Delta decision-makers, agency managers, stakeholders, the scientific community, and the public. Numerous academic institutes also play major roles in Bay-Delta research, including the UC Davis Center for Watershed Sciences and the UC Davis Coastal Marine  Sciences Institute.

How is scientific research funded?

Funding for scientific research in the Delta comes from numerous sources, including government (federal, State, and local), non-government organizations, and private interests. In general, it is difficult to obtain funding information on all scientific research as it is rarely separated out as a budget line item. It is also challenging to find funding information on restoration and other system-wide investments. For example, public sources like the Federal Crosscut Budget are not revised over time to reflect actual spending; however, it is useful in providing an estimate that can be compared with other Federal Crosscut budgets in other systems.

For FY2016, federal agencies budgeted $372 million for the Bay-Delta Program. For reported years 1998-2017, average annual budgeted funding has been $314.7 million and totaled $6.294 billion. For FY2000-2012, State agencies provided, in total $3.258 billion and on average $250 million in funding for the Bay-Delta Program. Public water agencies and the State and Federal Water Contractors Agency also play major roles in funding and implementing restoration and scientific research, as well as quasi-private organizations like water districts.

The Council has recently launched DeltaView (, a new database that will capture and track State and federal spending on programs, plans and projects in the Delta, as well as project goals and project descriptions, cost and funding sources, key dates, responsible agency, and relevant performance measures. DeltaView will provide implementing agency users the opportunity to update their records on an ongoing basis, and allow the broader public the ability to track progress toward Delta Plan implementation.

California Bay-Delta Presentation

Presenter: Dr. Ted Sommer, Lead Scientist, California Department of Water Resources.  Research interests include aquatic ecology, floodplain ecology, native fish restoration, and salmonid biology.

Presenter: Dr. Josh Collins, Chief Scientist, San Francisco Estuary Institute (SFEI).  Research interests include landscape ecology, regional ecological planning, mapping/assessing stream and wetland ecosystems, restoration, and monitoring.

Dr. Ted Sommer

The Delta is a tough nut to kind of crack,” began Dr. Ted Sommer. “We can talk about the basic geography and where it is but to be honest, a lot of folks that live right next to the Delta don’t even realize they’re right next to the Delta. We can talk about the statistics. It drains almost half of the state, it has 1000 miles of levees, it has 60,000 acres of open water habitat, but even that really doesn’t get you to the kind of sense of place. One of the best ways to come to grips with the Delta and how science is constructed around it is really to go straight to the extremes.”

Most deltas have a river that drains from inland and fans out into the ocean. “The gods were clearly drunk when they did our Delta,” he said. “They put the Delta facing the wrong way and that has all kinds of consequences for hydrodynamics and management.”

When we do landscape alteration here, we do not mess around,” said Dr. Sommer, presenting a graphic from the San Francisco Estuary Institute comparing the historical Delta to the modern Delta. The historical Delta was dominated by tidal wetlands with complex small channels; in contrast, the modern Delta is dominated by agriculture.

In California, most of the precipitation falls in the northern part of the state, while most of the population lives in the southern part of the state. California has the sixth-largest economy in the world. This is all driven by hydrology, said Dr. Sommer.


Most of the inflow into the Bay Delta comes from the Sacramento River, although there is inflow from some of the other tributaries as well; some of it actually makes it out to the San Francisco Bay; most of it is redistributed to other areas where a lot of the population sits. All or a portion of the water supply for 25 million people comes from the Delta.

Dr. Sommer said the Delta has a lot of barriers and gates, with some unusual uses of the different barriers. One example are the Suisun Marsh salinity control gates, which are operated to tidally pump fresh water into the Suisun Marsh, one of the largest contiguous marshes. The Delta Cross Channel is a large channelized corridor in the central Delta; the Cross Channel gates help control when fresh water and fish get into the central Delta. In the south Delta, there is a network of barriers because of the elevation changes from all the diversions; the gates there are needed to maintain elevations.

Fresh water diversions are the one thing that is different than any of the other systems presented at the workshop.  There are large diversions from the state and federal water projects as well as a couple thousand smaller agricultural diversions which play a large role.

However, the big challenges don’t stop there, noted Dr. Sommer. Climate change is an emerging issue. Because of the state’s climate variability, the hydrology alternates between flood and drought. On top of that, the landscape is gradually subsiding with parts of the Delta 25 foot below sea level, just waiting for a big earthquake or flood.

Given the amount of changes that have occurred and the challenges facing the Delta, there are a whole suite of native species that are in trouble: spring run and winter run chinook salmon, the delta smelt, the longfin smelt, steelhead trout, and green sturgeon.

Collectively, the status of these species is a really big deal in both the science and management,” said Dr. Sommer. “I would characterize, given how important water is in the state and the effect these species have on management, these are the most economically important fish species we have in the United States.”

There are also problems with invasive species. Recent estimates from UC Davis are that 30 percent of the open water in the Delta has aquatic weeds. There have been major benthic invasions that have transformed the food web so the fish communities are shifting rapidly. “We’re seeing a move away from pelagic communities towards more benthic and inshore communities, and a lot of those are driven by invasive species,” said Dr. Sommer.

Water quality is another major science and management issue. With the agricultural economy, there is an ever-shifting array of different contaminants that are coming in the system. There are issues with nutrients, and harmful algal blooms have become a serious issue. “This year in particular, we’ve seen some of the most striking harmful algal bloom issues in the South Delta, but also statewide in places where we’re redistributing the water,” said Dr. Sommer.

The institutional complexity is also extreme. It may not appear to have any structure, but it’s somewhat clearer when you look at the central players. “We do have some organization, but it just does give folks a sense of all of the challenges we have in balancing both the resource management and the science,” said Dr. Sommer.

There are a lot of groups involved in science in the Delta. There are universities, such as UC Davis, San Francisco State, UC Berkeley, and UC Santa Cruz who are involved heavily in the research. The agencies play a huge role in the monitoring, so there is a broad collection of both state and federal agencies involved. There are also a number of NGOs, consultants, and public water agencies who are also contributing to the science.

With so many issues and so many different agencies and organizations involved, Dr. Sommer acknowledged that it is a struggle to collaborate and work together. There are individual efforts like the Delta Science Program that provide some overall vision; the Delta Regional Monitoring Program tries to provide cohesiveness to some of the key water quality issues; and the Collaborative Adaptive Management Team (CAMT), which is an effort to keep some of the key parties that have been warring over water issues out of the courts.

The state and federal water contractors do their best to pool resources. The Interagency Ecological Program (IEP) is the most cohesive effort, bringing together a suite of state and federal agencies with a nexus by which the public and stakeholders can participate, but also a series of agency layers that allow managers and directors to provide input as well.

Dr. Sommer noted that none of the efforts include co-location. “Personally, one of the things I believe is that co-location is a big deal for science – getting a critical mass of scientists together that can work together,” he said. “We’re working towards building a new IEP field station where we can at least co-locate a lot of the monitoring efforts that we’re doing right now, and hopefully build some synergies, but again, co-location is not currently a part of the program.”

Dr. Sommer then presented a list of science topics, sorted into things that are done well, things that are done terribly, and things that are rapidly improving. “In the terrible column, I think most folks would agree we’re pretty bad at doing things like contaminants, and some of the small invertebrates,” he said. “We actually do a pretty good job on relative measurements of some of the fish species and distribution. We’re really good at some of the basic water quality functions.  We’re really good at flow, and kind of okay at invertebrates and phytoplankton.”

Much of the innovation in monitoring includes non-lethal sampling as there are so many different listed species to deal with and looking at off-channel habitats as much of the program is designed around channel habitats. Our capabilities on synthesis are improving. There is increased use of continuous sensors. “In the phytoplankton area, I wanted to emphasize new efforts to look at harmful algal blooms and macrophytes,” Dr. Sommer said.  “That’s the most vibrant area of science right now in my opinion.”

Dr. Sommer presented a graph showing funding for science activities in the Delta, noting that it’s an estimate and does not include NGOs, utilities, and contractors. “There are other sources, but this is a reasonable, relative approximation,” he said. “Since 2000, there’s been a general increase in funding. Also the funding sources aren’t particularly diversified. In the Delta, it’s mostly coming from three different agencies: the Bureau of Reclamation, the Delta Stewardship Council, and the Department of Water Resources.”

The budget for the Interagency Ecological Program has been relatively stable, but the number of issues has increased steadily, Dr. Sommer said.

Dr. Sommer noted that there’s an imbalance in the way a lot of the science is being done in the Delta. “This is my opinion, but if you break down the budget for the Interagency Ecological Program into compliance, directed studies, synthesis, and modeling, more than 70 percent of our budget is just going into compliance and monitoring of standard things.   We are making improvements on synthesis, and we still have some directed studies, but there’s a sliver you can’t even really see, which is solicited research. We’re not doing much in the way of solicited research. That was not the case historically; we did historically have funds available for that. Our compliance costs have gone up and up, our budget has been flat, and the net effect is the compliance and monitoring takes a larger piece of the puzzle.”

Dr. Josh Collins then took over the presentation, noting that he’s going to look downstream and then look upstream.  “We’ve taken this system and found some way to carve it up, and we are working to put it back together again,” he said.  “Those of you who are from outside the region, this is a call for help. Most of you look as though you’ve done a better job for a longer period of time of trying to put your systems back together again and we’re on that trajectory, but we have some ways to go.”

He presented a map of the Bay Delta system, noting that he sometimes calls it the Greater Golden Gate Ecosystem, but the name hasn’t caught on. There are three principal Delta watersheds, the Delta itself, and the San Francisco Bay and its watersheds. “We also have the Gulf of the Farallones that never gets talked about, but if you’ve ever had the pleasure of going in or out the Golden Gate, you’d know that it’s a long way out from the Golden Gate before you get away from the estuary. It’s a long way before the water turns color, before you feel as though you’re actually away from the influences of that Greater Golden Gate Ecosystem. Arguably, the Gulf is part of it.”

The San Francisco Bay Area is a big place in terms of the number of people and in terms of an economic engine. It’s also a big place ecologically, in terms of number of rare and endangered species. It’s only been around for five or seven thousand years and there’s been endemism in that amount of time. The modern environmental movement was based, in part, on the Bay Area; it’s all part of the legacy.

There’s always enough money in this magical place for so many bright people to get something started that then peters out,” Dr. Collins said. “It’s very hard to get a consistent and coherent focus that lasts more than two or three one-off something-or-others, so part of what we’re dealing here was just too much money, too much intelligence, not enough time, and everybody trying to do the best they can. That’s an underlying theme in the Bay Area: entrepreneurial endeavors though horizontal organizational structures, both public and private. The idea of disruptive boundary organizations with flat organizational structures was invented here. Why? Because nobody here wants to work for anyone else. And we’re proud of it.”

Dr. Collins then turned to the history of the Bay, noting that it’s his version of the history of the Bay Area; other people could tell a different story. “One of the things that happened was the EPA walked into the San Francisco Bay and said, ‘This is a national estuary.’ People said, ‘I beg your pardon? What is the national estuary?’ ‘Well, you qualify for the National Estuary Program (NEP). We’ll dump some money on you to figure out how it doesn’t work, and then how to fix it, and you’ll keep getting some money until you have the capacity to carry on by yourselves. If you agree to that and you manage to produce a Comprehensive Conservation and Management Plan (CCMP), and if the governor signs, and it then goes to the EPA, and if the EPA Secretary signs it, it then becomes an instrument of the Clean Water Act. Then you have something you can use to hold yourselves accountable to each other.” All of that happened, and we’ve been trying to live up to it ever since.”

The CCMP, sponsored by the EPA, began big. It encompassed the Delta and its watersheds. And it hit political walls, and then the focus fell back to the Bay Area. While the San Francisco Estuary Partnership is recognized as a National Estuary, it does not include the Delta.  “That decision to scale back to the Bay, however it was made, just perpetuated the problem that we’re trying to overcome now,” he said. “We have a legal instrument still on the books. The CCMP gets updated, most recently this year. It always talks about the whole system; but always gets applied mainly to the Bay Area.”

In 1993, a regional research strategy was prepared as part of the CCMP that supported creation of the SF Bay Regional Monitoring Program (Bay RMP). It focuses on ambient monitoring around San Francisco Bay and Suisun Marsh for the purposes of determining whether the National Pollutant Discharge Elimination System (NPDES) permits for sewage treatment plants and storm drain systems are actually working. “Are those individual, end-of-pipe permits adding up to something better for the bay? The RMP decides whether it is,” said Dr. Collins. “It’s a very important program, but it’s driven by the US Clean Water Act and therefore emphasizes pollution monitoring.”

Dr. Collins said the community has been trying to integrate ecological considerations into the monitoring program by emphasizing the need to monitor the beneficial uses of the waters, which includes wildlife support, and not just the chemical stressors. The community has also set regional goals for subtidal and intertidal habitat and has called for a program to monitor progress toward the goals.

Dr. Josh Collins

We’re on the verge of maybe having a regional wetland monitoring program, after 25 years of trying,” he said.  “It was called for in the original CCMP; maybe now we get it. Those of us involved with this initiative have said, ‘Let’s do the Delta, too’ and the agencies’ answer has been, ‘No, not yet.’ We’re still trying to create a wetland monitoring program in either the Delta or Bay that can be expanded across the entire system, but we continue have trouble with funding. The need is clearer than ever, given the large amount of funded wetland restoration, so perhaps the monitoring will follow.”

Dr. Collins said if they can get more regional monitoring programs going, which is what they are aiming for, they will likely be designed to support coordinated environmental review and permitting at regional and landscape scales. “If we can get rid of the ridiculous balkanization of the system we might be able to coordinate restoration planning and management of the system as a whole, as intended through the CCMP. We can get all the way back to caring for the whole system again,” he said. “But the real charge now, the frontier of both environmental science and monitoring in the Bay, is the regional approach to watershed-based coordinated environmental review and permitting across water quality, flood management, and wildlife conservation. There is a growing need to better coordinate regulatory procedures across the Clean Water Act and Endangered Species Act at ecologically meaningful scales, as necessary to adapt regulation to shifting baseline conditions due to climate change and population growth.”

Climate change, sea level rise, drought, and deluge are creating a climate of change where regulators and managers are saying, ‘How are we going to deal with this?’, and they say ‘Not by ourselves. Not individually,’” said Dr. Collins. “At what scale do we coordinate permitting? You can’t get rid of permits; they protect the relationship between people and the environment. And you can’t integrate them. That’s against the law. So, they have to be coordinated. At what scale do we coordinate environmental review and permitting, so that we can get ahead of these issues, and not be slowing down our restoration work with necessary but slow and inefficient environmental review and regulation?

Dr. Collins said that in the Bay Area, they think in threes: such as past, present, and future; or federal, state, and local. “It doesn’t do any good for science to reach across to only one level of government, because in this country, you have to integrate vertically,” he said. “Environmental laws are implemented mostly by local agencies. That’s where land use happens, and land use controls the environment, so you have to integrate vertically through government from federal agencies to local jurisdictions. We’re aware of that in the Bay Area – not that we do it well, but we tend to think federal, state, local when we envision policies, their implementation, and science support.”

Another set of three perspectives is near-term, midterm, and long-term.  “We try to keep the big thought out there in front of the immediate thinking, to know where we need to be in 5, 10, 20 years or beyond. Then we try to take the baby steps in that direction,” he said. “There are no home-runs in government. There’s a lot of singles. It’s important to know when the bases are loaded. There are other triplets as you can imagine: the three laws of thermodynamics; me, you, the other guy; w, y, and z. This is the practical way we organize everything we do. On the science side, on the policy side, and on the public side, we really seem to think in threes.”

Like the other regions represented here today, including the Delta, the San Francisco Bay has also been transformed: 85 percent of marshlands around the Bay have been converted to non-tidal commercial uses. The historical ecology report referenced earlier came about because there were a lot of people fighting over what this or that piece of land should be next; they couldn’t agree, so a program was created to reconstruct the past in compelling detail in a geographic information system. It lives on with additional information because everybody loves the historical past,” Dr. Collins said.  “Everybody shares the history of family and place, and they hold no guilt about the past. We have found, quite surprisingly but wonderfully, that people who are fighting tooth and nail over what should be done with some piece of land will work together to learn its natural and human history, to literally map their discoveries, or re-discoveries, become associates or even friends, and start envisioning the future together.

Dr. Collins noted that the past isn’t something you can reach; ecosystems don’t run backwards. “When you do the historical ecology, you can see what you used to have, and you understand how things have changed,” he said. “You know what you can manage and what you can’t manage, and you can aim for things that you can really do. The past matters, not because you can reach it, not because you can reproduce it, but because it informs your thinking about what the future could and should be.”

Why are we focusing so much on wetlands?” Dr. Collins asked. “Wetlands matter for lots of scientific reasons. For one thing, everybody meets there,” Dr. Collins said. “Lots of environmental policies, both terrestrial and aquatic, meet or collide in the wetlands. They really are transitional areas, not just in ecological terms, but in political terms. They’re very sensitive to surrounding environmental change, both intentional and otherwise. So, they can be difficult to fully restore. They’re good indicators of environmental conditions and problems. They’re also important unto themselves, for many celebrated reasons. If you can bring the wetlands back, you can do other things.”

In the Bay Area, the community of wetland interests is quite literally following the Clean Water Act and Endangered Species Act from the bay waters to the wetlands and into watersheds. “We’re just following the flow upstream, and slowly, maybe too slowly, we’re understanding the need for a watershed approach to wetland protection, and therefore a watershed approach to coordinated regulation,” Dr. Collins said.

The key science topics in the Bay Area are fresh water supply, sediment supply, water quality, population growth, sea level rise, and many of the related topics. For the Bay as a whole, most of the freshwater flows and coming through the Delta, but that’s not the whole story. “It’s the unnatural timing and lack of variability in Delta outflows to the Bay as well as their volumes that are impacting downstream ecology,” Dr. Collins said.

He presented a 10 indicator bay fish index as an example of the kind of synthesis done to assess Bay conditions. “Bay scientists put together an ‘uber’ index of fish health based upon numerous species that shows the declining condition upstream in the estuary and over time,” he said. “But there’s still much more to the story,” he said. “The Bay is fed by numerous local streams and each one has its own little estuary. They matter a lot in terms of their ecological services and cultural resources,” Dr. Collins said. “We see the Bay as a complex of many small estuaries, each belonging to a local watershed, and each providing sets of services that contribute to the Bay’s environmental wealth.”

The sediment supply is mainly coming from local watersheds rather than the Delta, but that wasn’t always the case, Dr. Collins said.  The throughput of sediment from the Delta used to be the largest supply, but that’s been turned off by upstream dams retaining a lot of sediment and a reduction in erosion off of land surfaces.

In the meantime, we still have erosion in watersheds around the Bay, so the local watersheds are now becoming the dominant source of fine sediment that we need for building marshes,” he said. “At the same time, we have TMDL (Total Maximum Daily Load) limits on fine sediment being imposed on local watersheds, telling people to turn off the supply of fine sediment from the watersheds. So, we continue to disconnected the Bay from its local watersheds through public policy and regulation.  We’ve disconnected the Bay from the Delta, and we’ve disconnected the watersheds from the Bay though policy and practices, despite scientific consensus that the Gulf, the Bay, the Delta, and their watersheds comprise one integral system with clear, physical, ecological, and economic connections.”

There are numerous chemical contaminants and other related water quality issues in the Bay. Through the Bay RMP, the monitoring data on contaminated species of estuarine wildlife eaten by people are converted into consumption advisories for the public. Microplastics are also a big deal; baseline measures of their concentrations in Bay waters were recently completed for the first time and the results show a greater abundance than in other estuaries.

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The Bay monitoring and research efforts have increased their focus on assessing the effectiveness of regulatory and management actions. “We are increasingly focused on the beneficial uses and services of the environment,” said Dr. Collins. “For example, with regard to contaminants, what we’re really caring about is not the contaminants themselves, but their level of impact on living resources. So, we monitor those resources. If they’re okay, we see no automatic need for research. If they’re not okay, we have to use research to understand the pathways of contamination and its manageable causes. We see targeted research as an essential aspect of a mature monitoring program, with the research being driven by the monitoring results.”

The nutrient story in the Bay is complex. There are nutrients coming out of the Delta, from local watersheds, and from wastewater treatment plants. There are a lot of storm water systems around the Bay. “We have a lot of nitrogen coming into this system,” Dr. Collins said. “The Bay is not as transparent as it used to be, before the advent of modern land uses that greatly increased the inputs of fine sediment. As we reduce these inputs, through entrapment of sediment behind dams and erosion control, the transparency of the bay will increase.  Light penetration will also increase, and algae and phytoplankton will be able to make use of the nutrient stores. The whole bay could turn green. Is that a problem? If so, how do we solve it? Do we retool all these public treatment plants and storm drains? That’s billions of dollars in retooling. So, we’re asking the question, is green bad? Probably green is not good, because there are harmful algal blooms involved with green. So, we can revise our question: ‘Where do we need to be on the system’s response curve to increased water transparency?’ We’re moving toward classifying conditions as poor, fair, good, based on what color the bay should be, and based on what color means in terms of environmental risk and management costs.”

Dr. Collins noted that the wastewater treatment plants are paying into a research program to see how much wastewater plants need to reduce their nutrient outputs to solve the emerging nutrient problem.  There are management options, he noted. In the south part of the San Francisco Bay, salt ponds are being restored to tidal marsh, but they can bleed chlorophyll and nitrogen out into the Bay system, so they need to be managed so they won’t augment the outputs from the wastewater treatment plants. “We’re realizing there are some options at the landscape scale for managing different parts of the system to help solve a problem,” Dr. Collins said.

With respect to sea level rise, a local consortium involving Point Blue Conservation Science is working with NOAA and USGS to produce models that integrate tidal flooding and river flooding at the margins lf the Bay. There are lots of people who are going to be affected by this flooding. “We know that the sea level rise estimates are going to be revised upwards, not downwards,” Dr. Collins said. “We know that the forecasts we’re dealing with now are probably low and the planning timeframe needs to extend further into the future. Sea level rise will not stop in 2100. We need to plan for higher waters over a longer period.”

The human population in the region is expected to continue to grow. “Sea level rise will squeeze the growing population between the Bay and the higher ground that’s steeper. The resulting socio-ecological issues are likely to intensify,” Dr. Collins said. “We wonder how we’re going to marry social planning to ecological planning.  How do you marry transportation planning with housing planning, with environment planning? The CCMP I spoke about is kind of a blueprint for the bay, but it’s not looked upon with the same authority or importance as the regional transportation planning, or the regional economic or housing planning, even though it probably needs to be on the same footing.”

Sea level rise in the Bay Area is mostly about the transition zone. That is the area of ecological interaction between the bay and its surroundings. There is very little natural transition zone left; most of it is urbanized. Only about 23 percent of the area that is projected to be impacted by sea level rise is actually undeveloped and protected at this time.

That means we have to move people, or somehow build a lot of levees around them, and the levees will have to be built over and over again,” said Dr. Collins. “And what about the railroads and freeways surrounding the Bay? Do we move them or elevate them or put them in tunnels or underground? Major changes in infrastructure are going to happen and they could be planned in concert with t-zone restoration.”

In terms of Institutional changes, we need to regard the estuary as a single system with many administrative divisions.  “There are different water quality boards that are regulatory agencies of considerable importance.  At every level of government there are multiple agencies for land planning, flood management, water supply, pollution control, and wildlife protection. There are essential environmental NGOs operating at local, regional, statewide, and national scales.”

“But everyone seems to recognize two parts to the estuary, magically meeting at a place called Broad Slough,” Dr. Collins said.  “If you’re on east side of that slough, you probably read the Sacramento Bee. If you’re on the west side, you probably read the San Francisco Chronicle or San Jose Mercury News. People of the Delta and Bay see themselves differently. The politics are managed differently. The cultures are different. That may not change. The challenge is to coordinate environmental science across the boundary, to the degree necessary to protect the whole system. The challenge is to create a Bay-Delta science enterprise.”

Dr. Collins said that the Bay does not have a science enterprise yet, but one is possible. It’s also possible to create an enterprise for the Delta. There is a danger that two separate enterprises might be created, with inadequate coordination between them. “Why does it matter?” asked Dr. Collins. “Obviously there are some large estuarine processes and functions that cross the boundary between the Bay and Delta. Estuarine transgression doesn’t care where that boundary is. Fresh water supply doesn’t care, nutrient loadings don’t care, sediment transport doesn’t care, anadromous fishes don’t care, maritime shipping doesn’t necessarily care. As scientists we’re aware of this, and we’re trying to understand the processes linking the bay and delta together, to explain the tonal nature of their transitions into each other, and better define their shared boundary or dissolve it.

Dr. Collins said bay scientific community enjoys many partnerships, including the private sector. “Increasingly, we’re reaching out to the major businesses and industries that are at risk because of these environmental problems, especially sea level rise, and we’re saying, ‘This is your issue, too.’ We don’t want Silicon Valley to move to Utah just because it can. Why are those CEOs here? Because of the aesthetic and environmental amenities. We garner their support; we have to protect the Bay as the aesthetic centerpiece of the region. We have to consider the emotional impetus for protecting the bay. Or we risk losing the progressive economic engines that help define the region. So, anti-up Google and anti-up wine country. You have a stake in the ecological health of the region, too.”

The Bay science community enjoys numerous internal partnerships and collaborations. Academia is a vital part of that community. Stanford, Cal, UC Davis, UC Santa Cruz, multiple State Colleges and some community colleges are increasingly involved regional and local environmental science issues. But the Bay doesn’t have a bona fide science enterprise, it doesn’t have an established a science forum. It doesn’t have something like the Delta Science Program.  The Bay has a number of enterprising groups, mostly centered on sea level rise, and they are starting to work together, and it’s really very important that an enterprise of science grows from these beginnings with a clear purpose that is either consistent or complimentary to that of the delta,” he said.

On the water quality side, it is clear that there is a need to integrate across management actions. “Water quality is the result of many things going on individually, and subject to varying levels of control. Point sources and non-point sources are large and complex categories of water pollution subject to varying controls that are inadequately coordinated. The focus on receiving waters almost always leads to upstream explorations that reveal multiple sources that must ultimately be addressed through politically challenging changes in land use,” Dr. Collins said. “With regard to habitat, we occasionally do ambient surveys of threatened and endangered species, just not very often and not always very well. The data tend to be variable and for most species we lack long enough or consistent time series to accurately depict trends. For most species, we lack understanding of thresholds for habitat distribution, abundance, patch size, and inter-patch distance.  The majority of the endangered species in the region depend on wetlands. We need a wetland RMP that fills in the gaps in our understanding about the population status and trends in these species. Since many of them will be tracking spatial shifts in habitat due to sea level rise and upstream salt water intrusion, the wetland RMP should extend between the Bay and the Delta.”

“In terms of sea level rise, we need to map and evaluate the “T zone,” and we need to get that started in the Delta,” Dr. Collins said.  “All the fundamental work by NASA and NOAA that enables us to identify the T zone hasn’t been done in the Delta yet. We cannot rectify tidal datums with geodetic datums in the Delta. We can’t run the tides over the land with sufficient accuracy to inform local sea level rise planning and response. That needs to be fixed.

With regard to sediment supply and tidal marsh restoration, the Bay science community has begun studying ways to augment natural sedimentation with various applications of dredged sediment. But, there also needs to be a comprehensive survey of all sources of sediment and a plan to efficiently exploit them. “Sediment is becoming a valuable commodity,” Dr. Collins said.

Overall, the Bay community of environmental scientists is moving into the social-ecological framework for integrating the natural and social sciences at large spatial scales. Public polling is becoming a more common tool to understand priorities, and there are growing efforts to involve disadvantaged communities in environmental plans. There is always a need to get more people directly involved in the plans that will affect their lives. Sea level rise provides a large opportunity to shorten the distance between environmental science, policies, and the people they affect. Consistent research and ambient monitoring is needed between the Gulf and the Delta for key concerns, such as wildlife conservation and water quality, with ample communication of resulting information to the public,” he said.

Funding for monitoring and related applied research is mostly driven by regulatory permits and is therefore project-based. Even the existing Bay RMP for water quality is permit-based. Funding for basic research comes through its own avenues, such as various programs of the National Science Foundation, US EPA, DOI, and in some cases state grants programs. Academic institutions have access to funds that are not available to regional monitoring programs except through partnerships with academicians. The basic research of our major academic institutions can inform monitoring programs in many ways, from the collection and analyses of data to their interpretation and visualization. “We can do a better job of aligning basic research with applied research,” Dr. Collins said.

Dr. Collins concluded by noting that the Bay-Delta community already has some great ways of communicating environmental science to the public. There are regular conferences and reports for individual programs, the San Francisco Estuary Magazine, the Pulse of the Bay, Bay Nature, lots of symposia and synthesis, and new online data aggregation delivery systems are forthcoming.

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