X2, OMR, Gates, Barriers, and more: Dr. Ted Sommer sorts out the hydrodynamics of the Delta

At the 2021 Bay-Delta Science Conference, Dr. Ted Sommer, the Lead Scientist for the CA Department of Water Resources, gave a short course on Delta hydrology, noting that hydrology is at the core of a lot of the work on science and management in the Delta and understanding the hydrodynamics in the system is necessary to be effective in the Delta.  This presentation aims to illustrate key points about the Delta, provide an understanding behind some regulatory criteria, and provide a simple conceptual model to help understand the general effects of future management changes.

Dr. Sommer gave the caveat that he is not a hydrologist; this will be a biologist’s interpretation of the key issues, but nonetheless, an effective way to look at things.  There isn’t a single source for this information, so links are provided for those who wish to dive deeper into the topics.

He then gave some key points:

  • The estuary is not a river.  For example, many who come from the Northwest want to apply their knowledge of Northwest rivers, but the Delta system is not riverine in several ways.
  • The Delta estuary is different than what people expect from estuaries, with some unique characteristics.
  • There’s no such thing as a free lunch.  The Delta has been highly modified, and all of those modifications have consequences.
  • Change is inevitable.

First, some geography …

The estuary has many different names:  Some call it the San Francisco Estuary, San Francisco Bay-Delta, Bay-Delta, or Sacramento-San Joaquin Delta.  To keep it consistent, Dr. Sommer said the whole system is the San Francisco Estuary.  In this talk, he’ll be primarily covering the Upper San Francisco Estuary, which has two parts:  the Delta, which is the region that extends from Sacramento in the north to roughly Stockton in the south to Chipps Island in the west, and the Suisun Bay region.  

People often lump these together as the Delta, but really, they’re distinct regions,” he said.

The origins of the Delta

The Delta is quite different from what other people call deltas in other parts of the world.  The picture on the top on the slide at the lower left shows what other deltas look like: the rivers flow out and fan out into a series of network channels.  However, California’s Delta is entirely backward from that; instead of fanning out into the ocean, the fan goes the opposite direction – inland.

This is because the origins of our Delta are different,” Dr. Sommer said.  “But the fact that our Delta is essentially backward has some really important implications for the way water works and the way organisms interact with this landscape.”

Dr. Sommer explained that the reason our Delta isn’t the typical fanned oceanward system is that the San Francisco Estuary was formed beginning about 15,000-10,000 years ago as the sea levels rose and moved inland, drowning river valleys and essentially created a network of channels. 

So there was the formation that occurred from sediments coming from upstream, but a big driving force in the formation was that sea level rise,” said Dr. Sommer.

A Delta transformed

Historically, the Delta was a vast network of primarily marshlands and emergent tidal marsh. Starting in the late 1800s, the Delta’s marshes were reclaimed for agriculture, creating the islands and channels that exist today.  Land use in Delta remains predominantly agricultural.  The San Francisco Estuary Institute’s report, A Delta Transformed: Ecological Functions, Spatial Metrics, and Landscape Change in the Sacramento-San Joaquin Delta, details the extent of these changes.

Historically, the northern region of the Delta region up had a lot of floodplain habitat, including what is now called the Yolo Bypass.  The Central Delta was a mosaic of different islands, and the southern Delta region had many small distributary channels that influenced hydrodynamics in various ways.

The modern estuary: A highly variable and altered system

Dr. Sommer presented a slide to illustrate how much the alterations to the Delta have changed the system.  The graph on the left is a hydrograph of the Delta, showing flows by month, with the historical Delta shown in blue and the modern Delta shown in green. 

What we see is that with the historical Delta, we had a longer or later and more prominent flow pulse that occurred. So typically, flows peak at a greater magnitude and later than they did historically.  Part of the reason is that the historical landscape was simply more complex; you had lots of off-channel habitats that buffered and slowed down movements across the landscape and delayed the peak in flows.” 

The other part of the reason is reservoir operations, as shown in the figure on the right.  “What that did compared to historical flows is reduced the winter flows by grabbing some of those peak events and discharging flows later. So, bottom line, our hydrograph here in the system is heavily influenced by the combination of the landscape and our reservoir operations as well.”

These changes vary significantly depending on the water year type.  The article, A comparison of outflow and salt intrusion in the pre-development and contemporary San Francisco Estuary, looked at different water year types.  

In the critically dry years comparing then and now is where you see the greatest difference,” said Dr. Sommer.  “So those differences between the years that are generated by the landscape buffering and reservoir operations are most prominent in those critically dry years and less prominent in the wet years. I hope you’ll look at the original article here to get a sense of how these numbers were generated. But it’s fairly informative in understanding how different water years influence the hydrograph in the system.”

It’s important to understand these regional differences and how the changes affected the system.  The slide shows the Delta then and now.  On the left, there is a complex network of fine channels with fairly limited capacity.  For flood management and land reclamation, the Delta has been modified to the much-simplified landscape with fewer channels, as shown on the right.

This is great for navigation,” said Dr. Sommer.  “It’s designed to try and convey floodwaters and move water efficiently as compared to the system on the left, which has probably a lot more microhabitats. So this might be part of the reason for that buffering effect with respect to the hydrograph.”

Many waterways in the Delta look similar to the slide on the lower left – big, deep trapezoidal channels designed to hold back the water, but not all are like this.  Some waterways will spill out onto floodplains in wet years.  The slide on the right shows two satellite images taken about a month apart in the early winter period; the waterways are shown in blue,  illustrating just how radically it can change in just a short period of time.

The critical role of the Yolo Bypass and its tributaries

The Yolo Bypass, a remnant of the historical floodplain that existed here historically, plays an essential role in flood management.  The Sacramento River flows in from the north, the American River flows in from the east, and the Yolo Bypass is the flood overflow basin for the system. 

The Fremont Weir, at the top of the Yolo Bypass, essentially acts as a low head dam or a berm; when the flow of the Sacramento River reaches a certain point, the water spills out over the weir and onto the vast floodplains of the Yolo Bypass.  The Sacramento Weir, located further downstream by Sacramento, is used only in the highest flow years as a flood outlet valve.  The floodwaters in the Bypass eventually drain back into the system near Rio Vista.

The hydrology of the Yolo Bypass is complex, with inundation possible from several different sources.  Dr. Sommer pointed out the smaller westside tributaries: Knight’s Landing/Ridge Cut, Cache Creek, Willows Slough Bypass, and Putah Creek.  When researchers started studying the Yolo Bypass in the late 1990s as a possible region for restoration, the assumption was that most of the influence would come from Fremont Weir and Sacramento Weir because by volume, that’s where most of the floodwaters enter the Bypass.

When they subsequently started taking aerial photos to understand better the landscape and how things were, they noticed something fairly remarkable.

“Here’s a natural color aerial photograph of a section of Yolo bypass, and what you can see are these remarkable colored bands,” said Dr. Sommer.  “These are the tributaries that have entered this landscape. And if I showed you the entire 40-mile expanse of the Yolo Bypass, you would see that from north to south, these bands persist the whole way, representing this lateral variability or lateral stratification.”

 “This was from a set of March 1998 photos, so we got curious and worked our way through a whole list of archival aerial photographs.  What we essentially found is that the bands are the rule, not the exception. When we went back and looked for each of these colored tributary bands, we see that in basically any set of aerial photographs during flood events where the photograph is remotely good, we see the bands.  This occurs in really minor flood events, only 8000 or 10,000, CFS, all the way up to the big, scary flood events like 1986.”

So this persistent banding is really a unique characteristic of a system.  There are other rivers some of you are probably familiar with where one river will come into the other, and you have a couple of bands that stay together. But this with four different tributaries that stay distinct for a 40-mile length is really quite unique.”

Why does this occur?  Dr. Sommer said that the Yolo Bypass is quite broad, up to six miles wide in some areas with water up to six feet deep or so, so it’s much like a thin veneer flowing across the landscape. 

If you took a cookie sheet and tilted it slightly and poured colored liquids from different points, they wouldn’t mix because it’s so shallow; there isn’t room or depth, if you will, to mix.”

The other effect of this lateral variability is its extreme effect on the amount of shallow water habitat.  The graph shows simple modeling for flow events in 1998 and 2000.  The green shows the shallow water area in the Sacramento River, which is negligible; the red line shows the vast area of shallow habitat created in the Yolo Bypass, so tens of thousands of acres of shallow water habitat are created even by modest flow events.

When the Bypass is fully flooded, it’s about a third of the area of all of San Francisco Bay. So it really is a key part of the landscape and the seasonality of the system,” said Dr. Sommer.

This is further explained in the research article, Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River.

Tidal variation in the estuary

Dr. Sommer reminded that it’s important to think about this as a tidal system and less as a river, as tidal variation and salinity variation are a key part of understanding the system.

The plot on the graph shows the salinity variation across different regions.  The left is the Bay; the salinity variation is relatively slight and remains so moving inland.   The salinity variation becomes significant once you get to the Suisun Marsh and Suisun Bay; the arrow shows how the ebb and flow of the variation, which changes over time.

Tidal flows and fish

There are also the spring and neap tides to be considered.  Spring tides occur when the moon and the sun are aligned; there is maximum tidal energy and the tidal differences are greatest – the highest highs and the lowest lows. Spring tides occur twice each lunar month all year long without regard to the season. Neap tides, which also occur twice a month, happen when the sun and moon are at right angles to each other. During neap tides, there’s a much more moderate tidal movement.  So depending on where we are in the tidal cycle, we can have very different conditions in the Delta.

He presented a figure of Suisun Bay on the upper right illustrating the tidal excursion that occurs there.  “This is reflected in the tidal flows, not just the salinity variation. There are many kilometers of tidal excursion in the main channels and a lot of tidal excursion that occurs within the marsh channels as well,” he said.  “A lot of organisms have adapted to deal with this sort of thing. It creates much more variability than we would have if it were just a static lake, or even if it was more of a riverine system.”

Dr. Sommer pointed out that this has real consequences for the organisms that try and navigate and survive in the system.  For example, when Chinook salmon are moving upstream, they are aimed at the Sacramento River.  Most maps depict the Sacramento River as a big channel, but there’s also the Deepwater Ship Channel that leads up into the Yolo Bypass in the same region.  There are fairly strong tidal flows in this area, so a fish trying to navigate to the Sacramento River will experience these tidal flows sloshing around on the order of 10,000 cfs, and there’s a strong tendency for the fish to move up into the Yolo Bypass instead, where fish passage is a problem.

It’s important to understand that looking at purely river flows here isn’t enough,” said Dr. Sommer.  “These tidal flows are often what the organisms we care about are seeing.”

It’s a similar effect for downstream, juvenile migrating fish.  The Sacramento Basin is the home to a lot of the salmon in the system.  There are young fish produced in the tributaries making their way downstream; they move down the Sacramento River where the tidal flows are significantly stronger and get hit by this huge tidal jet, which can push the fish up into the North Delta Cache Slough Complex. 

Dr. Sommer noted that acoustic telemetry has found that fish will often migrate down the Sacramento River and get jetted back up into the North Delta Cache Slough Complex, so there’s a hydrodynamic reason why a lot of fish end up there.

This is particularly important in drier years when flows are low in the Sacramento River.  There isn’t a lot of habitat in the Sacramento River, but because of the large tidal action at the base of the Bypass, there continues to be fish habitat well into drier months.  So having this tidal effect where fish are somewhat guided into the North Delta could be a benefit.  

The publication, Effects of Extreme Hydrologic Regimes on Juvenile Chinook Salmon Prey Resources and Diet Composition in a Large River Floodplain, documents how heavily used the North Delta area is in the wetter years and how the tidal flows helped guide them up there, and provides an excellent example of how understanding hydrodynamics guides our understanding of why fish use certain areas.

X2 and habitat

Understanding X2 is fundamental to understanding the regulatory environment of the Bay-Delta and the conceptual model of the low salinity zone where salt and fresh waters mix.   

Simply put, X2 is the distance of 2 ppt salinity from the Golden Gate Bridge. The graph shows some example distances.  A low number for X2 occurs in high flow years, when the salt field is pushed well downstream, down towards the Golden Gate Bridge.  An X2 of 55 is closer to the Golden Gate Bridge.  In low flow years, X2 is often a higher number as the salt field intrudes.

Dr. Sommer explained that one of the main reasons for having X2 is that it is a heavily managed system and the salt field moves around a lot.   Measuring the net volume of Delta outflow is difficult with the tidal flows, spring and neap tidal cycles, and other factors.  However, we are good at measuring salinity, so X2 provides an index for where the salt field is. 

One of the things we know is depending on where that salt field is that it really affects the amount of habitat area,” he said.  “That’s habitat area based on just salinity not based on the amount of food or other things, but it’s it gives a starting point.  When the salt field is further downstream, and it moves down towards Suisun Bay, there’s more habitat area that opens up, whereas when it’s inland, the salt field is stuck in some narrow riprap channels, so there’s less volume and less habitat area.”

This is one of the key reasons why X2 is used as a conceptual basis for some of our regulatory approaches. The hypothesis is that some of the species we care about will have more habitat area when X2 is downstream; of course, this varies by species, and it’s really complicated.  Habitat areas are only one part of the picture. But it gives you a sense for why there’s a heavy focus on X2 and why it’s been incorporated in some of our regulatory systems.”

More information on this can be found in the research paper, Variation of Fish Habitat and Extent of the Low Salinity Zone with Freshwater Flow in the San Francisco Estuary.

Gravitation Circulation and the Entrapment Zone

The concept of X2 came out of an older conceptual model of what was based on what people understood from other estuaries where mixing zones occur where salt and fresh water mix; there’s often a turbidity maximum and many species there.  So one of the mechanisms that was known from other estuaries is that there’s a two-layer flow that occurs in the mixing zone.

The slide shows a conceptual model from David Schoellhamer & Jon Burau of how this essentially works.  The graphic shows a cross-section of a river channel; there is freshwater flowing towards the Bay and seawater pushing in. 

Essentially, what happens is that when this freshwater comes down towards the bay, because it is lighter, it flows over the top of that saltwater,” explained Dr. Sommer.  “But some of that freshwater in the top mixes with the saltwater. And because of something called conservation of mass, you can’t have that water floating on the top and mixing without some corresponding effect. And the effect is that there is a net landward current so that water floating on the top helps create a lower layer movement upstream where there’s a current.”

This is called gravitational circulation because you have this top layer that’s flowing seaward, and you have a bottom layer that’s flowing landward in other estuaries. A lot of organisms have learned how to surf these different tides to help maintain their position. So this was our old conceptual model of how our system worked because we saw the two-layer flow and the turbidity maximum.”

However, when the USGS and others studied it further, they discovered that it didn’t really work quite the way we had thought.  “In particular, there is gravitational circulation, but it’s nowhere near as persistent as we thought, and it tends to be fairly localized,” he said.  “One of the areas it’s more persistent is farther downstream around the Carquinez Bridge, where there’s a big depth transition.  In the area of Suisun Bay, where we thought there was this gravitational circulation and two-layer flow that occurred, gravitational circulation wasn’t as common as we thought.”

A lot of folks that come to our estuary expect this whole gravitational circulation effect to be the dominant factor in how organisms moved, and in Suisun Bay, it is indeed really, really important.  And there flow patterns out there are really important. However, the gravitational circulation, as envisioned when I started working in the system, isn’t quite the dominant factor that we had thought.”

The USGS Fact Sheet, Summary of Findings About Circulation and the Estuarine Turbidity Maximum in Suisun Bay, California, provides more details. 

Water distribution system: Components and effects

The big issue with the water distribution system is that most of the precipitation in California falls in the northern half of the state, and most of the population is in the southern half of the state.  

Another challenge is the extreme precipitation variability.  The map in the upper left of the slide, generated by Dr. Mike Dettinger at USGS, shows the variability across the years and illustrates how California has the most variability than anywhere else in the country.

Most of the water flowing into the Delta comes from the Sacramento River.  The San Joaquin River, although fairly large, contributes much less in volume than the Sacramento River.  The east side tributaries do contribute some water as well.

Where does that water go?  The majority of the water flows out to the Bay, but a substantial amount is exported to support municipal and agricultural uses in the Bay Area, San Joaquin Valley, and Southern California.    

The Public Policy Institute of California has a fact sheet, Water use in California, that breaks down water use by sector and region.  In places such as the San Francisco Bay Area, the majority of the water use is urban.  Farther north, most of the water use is environmental. And in the southern part of the state, agriculture and urban uses tend to dominate.  Water uses vary by water year type: In wetter years, there’s a lot more water available for the environment; in drier years, more water is used for agriculture and urban uses.

The State Water Project and the Central Valley Project are the two large water systems that export water from the South Delta.  Within the Delta, there are about 2000 different water diversions that are lightly regulated, and how much water diverted is rather hazy.  However, it is known that the diversion occurs seasonally. 

A simple model to understand hydrodynamics in the Delta

To help understand how the system works hydrodynamically, Dr. Sommer provided a simple model to help understand what happens when water is pumped from the South Delta and how the different sources work.

The conceptual model for the effects of the South Delta pumps is based on a hierarchy that starts with San Joaquin River flows. When water is pumped from the South Delta, the hydrodynamic draw is greatest on the San Joaquin River, so the pumping first pulls water from the San Joaquin River Basin.

Once those flows are maxed out, if pumping rates are moderately high, the pumps will start pulling water from the north through the Central Delta, through the Old and Middle River, or the Mokelumne River Corridor.  And lastly, if the pumping is at a  very high rate, or if those two inflows from the two other sources are constrained, the pumps will start pulling water from the west Delta.

He reminded that this is all a tidal system, so there’s a lot of sloshing going on; it’s not a simple linear conveyor belt going in each direction.

Dr. Sommer acknowledged that how the flow patterns work is very complicated.  To understand the integrated effects of pumping and the hydrodynamic draw, flows in the Old and Middle River (OMR) in the Central Delta are monitored.  Old and Middle rivers integrate the hydrodynamic effect of each of the three different sources and so OMR is therefore used as a key regulatory and operational tool.

What are the implications?

Dr. Sommer then explained how these flow dynamics are interrelated.

The I/E ratios are another management tool in the Delta. Flows from the San Joaquin River are important because that’s the first level in the hierarchy; that’s where the pumps initially draw. 

The Delta Cross Channel is important for flows through the Central Delta because there aren’t enough flows from the San Joaquin River under a lot of circumstances, and so having a more direct channel from the Sacramento River helps keep flows moving down towards the pumps.

These hydrodynamic factors are why flows can reverse in the Delta.  If there’s insufficient inflow from the San Joaquin River and the central Delta OMR corridor, the net flows can reverse.

All of these factors speak to why understanding the effects of exports is so complicated. Any one of the three parts of the hierarchy can have a significant effect.

Dr. Sommer pointed out that the North Delta and Yolo Bypass region also have seasonally reversed flows.  “I talked about the high flow periods when flows are downstream, how it acts more riverine as a floodplain. But what happens during the drier season is that there are both ag and urban diversions that divert a fair bit of water and seasonally create net negative flows in this area.  Since this is such a biologically important area, that has interesting implications for restoration and flow management in the system.”

Gates and barriers

Dr. Sommer then turned to some of the unique features in the Delta, noting that there’s no ‘free lunch.’ “We’ve made many changes to the system, and we’ve tried to make things work a little better, but anything we do here has consequences,” he said.

The Delta Cross Channel

The Cross Channel was built to provide more flow down into the Central Delta and toward the pumps.  But one of the unintended consequences of the Cross Channel is that salmon migrating down the Sacramento River have a greater probability of moving into the central Delta area where the habitat and survival are poor, and the risk of entrainment or losses at the pumps is high.

One protective measure that has been taken for a while is the closure of the Delta cross channel to block off that movement and help keep endangered salmon in the Sacramento River so they can safely get out,” said Dr. Sommer.  “But by doing so, we’ve constrained this central Delta flows. And essentially, what that means is that we put increased pressure on this third tier, and so you have the potential for increased reverse flows in the west Delta.”

Suisun Marsh Salinity Control Gates

One of the things realized early with the construction of the State Water Project was that exporting more fresh water from the Delta would result in more salinity intrusion.  So the Department of Water Resources, with support from the Bureau of Reclamation, built the Suisun Marsh Salinity Control Gates in Montezuma Slough.  On the ebb tide, when fresh water is rushing through the system, the gates are open, allowing the fresh water into Suisun Marsh; once the tide starts to reverse, the gates are closed, blocking the seawater from intruding.  It essentially acts like tidal pumping to move more freshwater into the marsh, which is important for waterfowl and habitat management in Suisun Marsh.

Reminding that there’s no free lunch, Dr. Sommer noted, “one of the consequences of this is when we push more fresh water out in the marsh, there’s more salinity intrusion that occurs from the Bay, so what that means is that we have to release more fresh water from the reservoirs or dial down the pumps to keep the salt field in a neutral position and not creep upstream.”

South Delta Barriers

There are also several barriers installed in different locations in the South Delta.  When the pumps are working, there is a strong draw that pulls the water toward them; this drops the water elevations in the South Delta channels, causing problems for agricultural diverters, causing their pumps to stop working as well as higher energy costs. So in a settlement with South Delta ag interests, a series of barriers have been installed to block some of the channels and help maintain water elevations. A barrier has also been installed at the Head of Old River to protect fish.

Remember, with our hierarchy, if we block more of the San Joaquin River flows, the water has to come from somewhere,” said Dr. Sommer.  “When we have increased draw through that second tier, it comes through the Old and Middle River Corridor.  This increased drafting can still have entrainment consequences. So this is something that seasonally done to help manage water levels in this region, but it has some pretty major effects on overall hydrodynamics in the system.”

Drought barriers

When the hydrology is critically dry, flows are very low, and the salinities creep further inland, the state considers drought barriers.  If unchecked, salinity can intrude into the Central Delta, and once there, essentially control of the Delta is lost. 

You can’t get that saltwater out easily,” said Dr. Sommer.  “We have to wait for the next big winter storm to flush it out. So it’s really important to try and keep the salt field downstream of this central Delta area. … Without the barrier, there’s a jet of saltwater that comes into the central Delta. And by putting a barrier in, it makes it harder for that saltwater to creep in.  This is somewhat close to a free lunch here. But putting a barrier in this neck of the woods does have consequences for things like algal production, aquatic weeds, and so forth.”

Sea level rise

With sea level rise and with the growing risk of extreme weather events, all of this can be expected to change, said Dr. Sommer.

The slide on the lower left is an example of the effects of sea level rise in the Suisun Marsh.  Essentially,  under some of the more dramatic scenarios, much of Suisun Marsh will be underwater.

Similarly, there are the Delta islands, which aren’t islands but more subsided holes surrounded by high water in the channels.  Because they are farmed, the soil has been oxidized, lowering the level of the land. 

There’s a very high risk that one or more of these islands will break in the near future,” said Dr. Sommer, presenting the slide at the upper right showing the risk analysis of the different islands.  “All it will take will be sea level rise, or a major flood or an earthquake, and we will lose quite a few of these islands. We can do what is being done in the Netherlands, building super levees to try and protect them, but the cost of doing that is extreme. So long term, the ocean is coming. And we have to prepare for it.”

The Delta Conveyance Project

This is a lot of the logic behind one of the key initiatives that is controversial,” said Dr. Sommer.  “My own Department is a proponent of this project, so please consider my comments with an asterisk, but part of the logic here is if we know the salty water from the Bay is going to continue to intrude with sea level rise or with breakage of some of the levees in the islands, it will be increasingly difficult if not impossible to continue diverting water and supplying water for 25 million Californians, where we do it now or at least how we do it now.”

So the concept of Water Fix (now the Delta Conveyance Project) is building a diversion further upstream, so that we can continue to provide water in the future as climate change and salinity conditions change. Of course, there are a lot of different aspects of this. And there are quirky hydrodynamic aspects of this. But honestly, long term, it will become increasingly challenging to try and maintain the current system as is. And Water Fix is our department’s proposal, at least for the water distribution system.”

Hydrodynamics and the regulatory framework

Dr. Sommer then gave some examples of how hydrodynamics and tools are used in regulatory frameworks.

He presented a slide showing some of the requirements of the Delta smelt Incidental Take Permit and biological opinion, pointing out that Old and Middle River (OMR) flows are featured heavily.  OMR is one of the key management tools to manage entrainment.  There are actions specified for summer through fall actions related to the Suisun Marsh Salinity Gates’ operation, and the reverse flows in the north Delta.  The long-term habitat changes that have occurred historically are among the key reasons for the requirement for significant amounts of habitat restoration that the permits are calling for.

For salmon, there are the Delta Cross Channel operations to try to protect fish moving through the Delta, and OMR flows are a tool to manage movements of fish, entrainment risks, and exports.  And the Yolo Bypass floodplain a key target for salmon restoration because it’s a habitat that provides conditions suitable for rearing in dry years due to the hydrodynamics, particularly in wet years when it floods, and a vast area of shallow water habitat is created.

Data and other resources

Two good resources for conditions in the Delta:

  1. The California Data Exchange Center (CDEC) installs, maintains, and operates an extensive hydrologic data collection network including automatic snow reporting gages for the Cooperative Snow Surveys Program and precipitation and river stage sensors for flood forecasting.
  2. The Bay-Delta Live website seeks to expand open and transparent sharing of information essential in understanding the complex and dynamic ecosystem of the Sacramento-San Joaquin Bay Delta. Bay-Delta Live provides information from multiple sources using enhanced visual interfaces.

Other tools

Dr. Sommer said he hoped that this presentation has given you a basic conceptual understanding of how things work, but also that it is very complicated.  Increasingly, models are being used to help us understand what’s going on and predict how things will change under different operations.  Some of those include:

For basic flow patterns, DWR has a simple accounting system called “Day Flow” that estimates daily flow in the Delta.  It has historical monthly information going back many years; it also has information on exports. It’s often a useful tool to understand some of the biological responses.

A model called CalSIM is a monthly predictive model that can help understand how changes in inflow or changes in operations will influence overall patterns. For more complex hydrodynamics, including tidal influences, there are models such as DSM II, and other tools that help give a multi-dimensional understanding of the more complex parts of the estuary.

Particle tracking algorithms are used to help understand how things move around the estuary and how that might change under different scenarios.

Click here to watch the video of this webinar.



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Salinities & X2

Feyrer, F., M. Nobriga, and T. Sommer. 2007. Multi-decadal trends for three declining fish species: habitat patterns and mechanisms in the San Francisco Estuary, California, U.S.A. Canadian Journal of Fisheries and Aquatic Sciences 64:723-734  Abstract access:

Gross, E. S, Hutton, P. H, & Draper, A. J. (2018). A Comparison of Outflow and Salt Intrusion in the Pre‑Development and Contemporary San Francisco Estuary. San Francisco Estuary and Watershed Science, 16(3). Retrieved from

Hutton, P. H, & Roy, S. B. (2019). Characterizing Early 20th Century Outflow and Salinity Intrusion in the San Francisco Estuary. San Francisco Estuary and Watershed Science, 17(2). Retrieved from

Jassby AD, Kimmerer WJ, Monismith SG, Armor C, Cloern JE, Powell TM, Schubel JR, Vendlinski TJ. 1995. Isohaline position as a habitat indicator for estuarine populations. Ecol Appl 5(1):272–289.

Kimmerer, W. J, MacWilliams, M. L, & Gross, E. S. (2013). Variation of Fish Habitat and Extent of the Low-Salinity Zone with Freshwater Flow in the San Francisco Estuary. San Francisco Estuary and Watershed Science, 11(4). Retrieved from


Sommer, T., W.C. Harrell, and T. R. Swift. 2008. Extreme hydrologic banding in a large-river Floodplain, California, U.S.A. Hydrobiologia 598:409-415.

Sommer, T.R., W.C. Harrell, A. Mueller-Solger, B. Tom, and W. Kimmerer. 2004. Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River, California, USA. Aquatic Conservation: Marine and Freshwater Ecosystems 14:247-261.

Sommer, T., B. Harrell, M. Nobriga, R. Brown, P. Moyle, W. Kimmerer, and L. Schemel. 2001. California’s Yolo Bypass: evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture. Fisheries 26:6-16.


Schoelhamer, D.H. and J.R. Burau.  Summary of findings about circulation and the estuarine turbidity maximum in Suisun Bay, CA.USGS Fact Sheet FS-047-98.

Diversions & Effects

Grimaldo LF, Sommer T, Ark NV, Jones G, Holland E, Moyle PB, Herbold B, Smith P. 2009. Factors affecting fish entrainment into massive water diversions in a tidal freshwater estuary: can fish losses be managed? N Am J Fish Management 29(5):1253–1270.

Herren, J. R. and S. S. Kawasaki. 2001. Inventory of water diversions in four geographic areas in California’s central valley. California Department of Fish and Game Fish Bulletin 179:343-355.

Kimmerer, Wim J. and Matthew L. Nobriga. 2008. Investigating Particle Transport and Fate in the Sacramento-San Joaquin Delta Using a Particle Tracking Model. San Francisco Estuary and Watershed Science. Vol. 6, Issue 1 (February), Article 4.  Full article access:

Kimmerer, Wim J. 2008. Losses of Sacramento River Chinook Salmon and Delta Smelt to Entrainment in Water Diversions in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science. Vol. 6, Issue 2 (June), Article 2.  Full article access:

Monsen, N.E., J.E. Cloern, and J.R. Burau. 2007, Effects of flow diversions on water and habitat quality; examples from California’s highly manipulated Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science 5, Issue 3 (July 2007), Article 2.


Kimmerer, W., Wilkerson, F., Downing, B., Dugdale, R., Gross, E. S, Kayfetz, K., et al. (2019). Effects of Drought and the Emergency Drought Barrier on the Ecosystem of the California Delta. San Francisco Estuary and Watershed Science, 17(3). Retrieved from


Bever, A.J., M.L. MacWilliams, B. Herbold, L.R. Brown, and F.V. Feyrer. 2016. Linking hydrodynamic complexity to Delta Smelt (Hypomesus transpacificus) distribution in the San Francisco Estuary, USA. San Francisco Estuary and Watershed Science 14(1). Available at:

Gross, E. S, MacWilliams, M. L, & Kimmerer, W. J. (2009). Three-dimensional Modeling of Tidal Hydrodynamics in the San Francisco Estuary. San Francisco Estuary and Watershed Science, 7(2). Retrieved from

Kimmerer, Wim J.; MacWilliams, Michael L.; & Gross, Edward S.(2013). Variation of Fish Habitat and Extent of the Low-Salinity Zone with Freshwater Flow in the San Francisco Estuary. San Francisco Estuary and Watershed Science, 11(4). jmie_sfews_13887. Retrieved from:

MacWilliams, M. L, Ateljevich, E. S, Monismith, S. G, & Enright, C. (2016). An Overview of Multi-Dimensional Models of the Sacramento–San Joaquin Delta. San Francisco Estuary and Watershed Science, 14(4). Retrieved from

MacWilliams, M., Bever, A. J, & Foresman, E. (2016). 3-D Simulations of the San Francisco Estuary with Subgrid Bathymetry to Explore Long-Term Trends in Salinity Distribution and Fish Abundance. San Francisco Estuary and Watershed Science, 14(2). Retrieved from


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