Salinity management in the Delta during times of drought

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At the July 25th meeting of the Delta Stewardship Council, council members heard a presentation on the challenges of managing the Delta’s salinity during times of drought.

Salinity in the Delta is largely a tug of war between the daily and seasonal tides pushing in from San Francisco Bay and the flow of fresh water coming down through the rivers and heading out of the Delta towards the Bay. Salinity in the Delta is regulated to protect municipal and industrial, agricultural, and fish and wildlife uses, and if the saltwater intrudes too far into the Delta, it can make the water unusable. Since the Department of Water Resources and the Bureau of Reclamation manage the most of the water stored in upstream reservoirs, as well as the flow structures and pumps in the Delta, they have the primary responsibility for managing salinity in the Delta.

On the panel are John Leahigh with the Department of Water Resources, Mark Gowdy from the State Water Resources Control Board, Cindy Garcia with DWR’s Municipal Water Quality Investigation’s Program, and John Herrick with the South Delta Water Agency.

Sam Harader, Program Manager with the Delta Science Program, began with a short video from the Bay Delta Live website to demonstrate how salinity changes and moves in the Delta over time. The video is based on the actual data from the first half of the year, with the blue representing fresh water and the red representing the more saline water. The video shows depicts how far salinity intrudes into the Delta at various times of the year.  Notice how the precipitation in February and March begins flowing down into the Delta from north from the Sacramento River and south from the San Joaquin River, pushing the salt water back to the confluence of the two rivers. In May and June, the animation shows how far the salinity intrudes absent the freshwater flows to push it back.


  • Note 1:  To view this animation at the Bay Delta Live website using the most recent information, go here:
  • Note 2:  To view this animation with Sam Harader’s narration, click here for the webcast video, and click on the icon for Agenda Item 10.  Sam presentation begins at about 2:40:00.

Mr. Harader then turned it over to the panelists.

John Leahigh, Principal Engineer for State Water Project Operations with the Department of Water Resources

John LeahighJohn Leahigh is the Principal Engineer for State Water Project operations, and is responsible for the day-to-day management, the annual operations planning, and the regulatory compliance and reporting activities of the State Water Project.

He began by saying that the subject of Delta salinity management is complicated and complex, but he would try to compress it down to a short presentation that will cover how the projects operate and how they develop the supply for the projects, how this affects Delta salinity, and the salinity standards themselves specifically, as well as the knobs that the projects have to turn to manage that salinity. He would then end with the unique challenges they are facing this year that hopefully they will not have to encounter next year.

Leahigh Slide 4Mr. Leahigh began with ‘Project Operations 101,’  explaining how the major water projects develop their water supply. “All the reservoirs – Shasta, Oroville, Folsom, and San Luis Reservoir – are storing natural flows that are in excess of all the other beneficial uses that are occurring in the winter and the spring,” he said. “That’s our opportunity to store that water so that we can release it later, typically summer and fall, to meet beneficial uses in the system. That’s an important concept, and it may be fairly intuitive and obvious, but it’s important to keep in mind when we look at some of the challenges we face this year, for example, on the stored water component of this picture.”

Leahigh Slide 6Part of that storage is for the beneficial uses of the customers of the CVP and SWP, but even before we can provide that supply to our customers, we have to connect the supply from the north to the customers in the south,” he said, presenting a slide showing the extent of salinity intrusion before and after the upstream reservoirs were built. “To do this, a large portion of that stored water needs to open up a fresh water corridor through the Delta so that the supply is usable throughout the year.” He noted that the graphic shows that they’ve maintained this freshwater corridor throughout the year.

Leahigh Slide 8The State Water Board determines what is excess in terms of beneficial use, and sets the amount of the natural flows that must be allowed to pass through the reservoirs upstream into the Delta to provide inflow and salinity management with the Bay Delta standards, he said. To protect beneficial uses in the Delta, the State Water Board develops a water quality control plan for the Delta, and then ties the Department of Water Resources’ and Reclamation’s water rights to meeting those standards that are set forth in the plan.

Leahigh Slide 9There are standards for fish and wildlife, for M&I use, and for agricultural use, and they vary geographically throughout the Delta, as well as by month and by year type, Mr. Leahigh said, presenting a graph of Bay-Delta standards by type mapped on a timeline. “This gives you an idea of all of the standards that are in effect with the operational and flow standards on the top in blue and the water quality standards on the bottom for the three purposes: M&I, ag, and fish and wildlife uses.” He noted that the water quality standards mostly deal with salinity, and that the ag standards are more geared towards the timing of the irrigation season, which is April through August, while M&I standards are in effect pretty much year around.

Compliance is measured generally on 14-day or 30-day averages and is tied in with natural tidal cycles that occur, and with the Delta being the interface between the fresh water and salt water flows at sea level, the tides drive the big tug of war between the salts and the fresh water, he explained.

Leahigh 3 knobsSince the tidal forces are out of our control, we can only manage the freshwater side, and there are three ‘knobs’ to do that, he said:

  • Reservoir releases: “It’s either in the winter or spring, we’re allowing so much of the reservoir’s inflows to pass through to provide inflow to the Delta to control the salinity; or in the summer and the fall, we’re releasing previously stored water to add to the inflow to the Delta to repel that salt water intrusion,” he said.
  • Delta Cross Channel Gate: “The Cross Channel gate makes more efficient use of that freshwater that is released into the Delta, and provides a more direct path to the Central Delta, and down Old and Middle River towards the export facilities,” he said. “That’s a key component – a key knob to turn.”
  • Exports: “We can modulate those to the extent that we reduce those exports we can increase the total Delta outflow and therefore control salinity in that respect,” he said, noting that this knob was not really available this year. “The fact that we were dealing with such low exports in June meant that wasn’t even a knob to turn. We were essentially already down at minimum levels of exports, so it did not allow us to react quickly to salinity events.”

Leahigh Martinez stageWe cannot talk about salinity management in the Delta without talking about the tides,” he said. He explained that there are two components to the tides: the daily cycle and a monthly cycle. He presented a chart of the stage at Martinez, noting that the location is right at the interface between the San Francisco Bay and the Suisun Marsh. There is a daily cycle of two ebb and flood tides per day, with a four foot difference between the ebb and flood tides, he noted.

If you multiply four-foot stage change throughout the surface area of the Delta channels – that’s a large amount of water that’s moving back and forth through that area, and so the result is the huge tidal flux that we see daily, twice per day, into the Delta, and of course the salts follow the flow.”

Leahigh flood-ebb magHe said that in the Suisun Marsh, they see tidal fluxes of over 300,000 cfs. “To put it into context, if 300,000 cfs were the inflow into Folsom Lake, that would essentially fill Folsom in a day and a half, so that’s the amount of flow that we’re talking about that’s occurring on a daily basis. Even things such as X2 position is something that’s not static, but is moving several kilometers per every few hours, twice a day, so when we talk about X2 position, for example, we’re talking about an average X2 position.”

On top of the daily flood-ebb cycle, there is the monthly neap-spring cycle that is driven by the orbit of the moon around the earth. “Essentially there are seven days of general filling of the Delta, followed by seven days of general draining of the Delta. On top of that daily cycle, there’s this monthly change as well, so the salts tend to creep in more prominently in the spring tides and less so in the neap tides.”

The tides that have been discussed so far are astronomical tides, and since they are based on the movement of heavenly bodies, they are predictable, but unfortunately, that’s only one aspect that drives the tides, he said. “The other aspect is meteorological conditions, which are highly uncertain and highly variable, so you get a storm event, you get a storm surge, you get the onshore winds associated with that, you get low barometric pressure, and all of those have bearings on the tidal changes.”

Leahigh Spring-Neap AntiochHe presented a slide of the stage of the San Joaquin River at Antioch. “What I have circled in red is where there was a storm event during this time period which overwhelmed the astronomical effects of the tide and so meteorological effects take over,” he said. “Why that’s important is that the projects need to respond to that sort of salinity event that may be created by that.”

Leahigh Travel TimesThere is a time lag with reservoir releases, he said, noting that it takes five days for the water to travel from Shasta, three days from Lake Oroville and one day from Folsom before there’s an effect in the Delta. Modifying exports has a quicker response and can generally affect salinity within a day with a reduction at the export facilities, he said.

Leahigh COAThe other question is where does the water come from when a change is necessary, he said. It could be a reservoir or it could be the export facilities, so Coordinating Operations Agreement (COA) is used to determine where the contribution is made from, he said. “The COA is in effect a water rights settlement agreement between the two projects as far as assuring the responsibilities for meeting the Bay-Delta requirements,” he said. “It dictates on a daily basis who is responsible for making up any shortages in the system and if there is excess flows, how those benefits are shared, so that agreement addresses both of those factors.”

Leahigh DCCThere are always trade-offs with the knobs and the Cross Channel Gate is a prime example, he said. “It’s better for water quality to have those gates open, but that interferes with the fish migration periods, so both in the water board’s water quality control plan and in the biological opinions, there are certain periods where we are not allowed to have the gates open. Of course, there’s a cost to that, both in terms of salinity and in terms of water supply, because essentially when those gates are closed, it becomes a much less efficient operation as far as getting the fresh water flows into the system to meet the standards and it requires either additional flow from upstream or less exports in order to compensate for a closure of that gate.”

Leahigh insuff storageThe overarching and specific challenge this year was the lack of storage, he said. “The storage that’s necessary to be gained in the early part of the year to meet all the beneficial uses later in the year, one of them being keeping that fresh water corridor open, was greatly compromised by the fact that as of late January, we had the driest precipitation on record for the Northern California and reservoir levels were extremely low. In fact, not only were we not gaining storage, we were still losing storage as of late January, so that was a huge concern.”

The water projects petitioned the Board for modifications of some of the standards in the spring in order to lessen the need for releases from the reservoirs, so as much water as possible could be kept to meet beneficial uses later in the year. “Some of those trade-offs would include temperature management, so some of that storage was necessary to build up the cold water pool so that we would be able to make appropriate releases to benefit the salmonid species in the summer and fall,” said Mr. Leahigh.

Leahigh drought barriersEmergency drought barriers were contemplated as we continued to see dry conditions after January and it was forecasted that there wouldn’t be enough storage to release from the reservoirs into the Delta to control salinity, he explained. “So as a crutch, the emergency drought barriers would at least mitigate the extent of salt water intrusion into the Delta because of lack of fresh water,” he said. He explained that the function of the two barriers north off of Sutter and Steamboat sloughs would be to raise the stage in the Sacramento River and push more of the limited fresh water through the cross channel into the Central Delta to make more efficient use of that limited fresh water, and the barrier at West False River would limit the salt water intrusion from the tides.

leahigh Clifton Court ForebayBecause of the above-average precipitation received during February and March, the drought barriers did not need to be installed, he said. He then presented a slide that depicted how salinity had changed throughout the year, using the EC at Clifton Court Forebay as an example. “Because of the lack of very low inflow into the Delta due to the dry conditions over the course of late fall into winter, into late January, EC levels continued to climb. We actually did exceed 1.0 for a period of a number of days as was the case at Jones Pumping Plant as well. That was not out of compliance with D 1641 because it’s based on a 30-day running average, so it was a couple days over but it did not exceed the 30 day average.”

You can see then the improvements on the salinity,” he said. “The lower graph shows the flows on the Sacramento River at Verona, and you see a number of natural pulses that occurred due to the rain and the runoff downstream of the dams. The dams, themselves, were at minimum releases, trying to store as much water as possible for use currently and in the fall. The amount of precipitation that we did receive in those two months was just enough for us to limp along and continue on through this year.”

We started to have some increase in salinity in June,” he said. “We were able to adjust our releases to insure that the salinity did not get to the level it did back in January, and that was because of the fact we were able to store a sufficient amount from February and March to offset that salinity increase.”

Going into 2015, one thing is that we’re going to be in a worse condition as far as storage is concerned, so storage levels in all the reservoirs will actually be lower going into 2015 then they were going into 2014, so of course that’s great concern,” he said. “The drought management tools we have on the table are the same ones that were used this year or that were contemplated to be used this year, so we would continue to look at very low delivery capabilities from the projects, more likely to be cutbacks or shortages to the settlement contractors this coming year, and we would also probably look at modified Delta standards if absolutely necessary, and at worst case, we continue to pursue the planning for possible drought barrier installation in 2015 as a last resort.”

Now we all hope we don’t end up there, but that’s sort of our contingency planning that we have in place should the need arise into 2015,” he said.

So that concludes the remarks that I had …

Mark Gowdy, Division of Water Rights, State Water Resources Control Board

Mark Gowdy then discussed the salinity effects on agriculture in the south Delta. He noted that his primary responsibility as a senior water resources control engineer is working on the phase one update to the Bay Delta Plan, which is focusing primarily on San Joaquin River flows as well as southern Delta salinity objectives and their implementation. In his presentation, he discussed how salinity in irrigation water affects crops, focusing on the southern Delta, as well as update what’s happening with the southern Delta salinity objectives.

Mark GowdySalinity, as it pertains to agriculture, is concerned with the concentration of various ions in the water,” he said. “Contrary to what the name suggests, it’s not just about sodium chloride. It’s about all dissolved ions, including calcium, magnesium, and others.”

A very convenient although crude way to measure these concentrations is to measure the water’s ability to conduct electricity,” he said. “With more positively and negatively charged ions in the water, electricity can move more readily and so measuring conductivity provides an indirect measure of the ionic concentration in the water.”

There are several different units for conductivity and it’s a source of confusion, he said. We often refer to salinity in terms of millimhos per centimeter (mmho/cm); agricultural literature uses deci-Siemens per meter (dS/m); and the municipal water community often uses microsiemens per centimeter, but the numeric values are all the same, he said.

Total Dissolved Solids is another way people have evaluated salinity, but it’s a rather cumbersome procedure, so measuring EC is quicker and is really the standard for research, objective setting and compliance, he said.

Under the Clean Water Act, Porter Cologne and other laws, the State Water Board is responsible for identifying beneficial uses and developing objectives for their protection, and the Bay-Delta Plan is the document where we identify those beneficial uses for the Delta and establish the salinity objectives, he said. These objectives are then implemented through water rights decisions, the most recent being D 1641, which makes requirements for meeting those objectives part of the water rights for the projects, he said.

Currently, the objectives for the Delta for salinity, and these are southern Delta, is .7 millimhos per centimeter (0.7 mmho/cm) in April through August as a 30-day running average of daily maximums, and then 1.0 mmho/cm for the months of September through March, he said.

In a court ruling in 2006, the State Board committed to reevaluating the salinity objectives, looking at the methodologies used to calculate soil water salinities in the development of the objectives, and in particular, take a closer look at how precipitation should be factored in, he said. As part of that effort, the State Water Board hired Dr. Glenn Hoffman, a nationally recognized expert on salinity who is retired now from the USDA Salinity Laboratory in Riverside, he said.

Gowdy Map South DeltaGeographically, we’re talking about the very southern tip of the Delta, he said, he said, presenting a map of the area. “The objectives that I had pointed out to you earlier apply at these four locations: the San Joaquin River at Vernalis where the San Joaquin enters the Delta, and then three interior locations as shown on the map.”

Salinity-related effects on crops can be broken down into three general categories, Mr. Gowdy explained: There is the stress that the salt in the soil water in the root zone puts on the plan; there are also effects if the ratio of sodium ions to other ions is too high because the sodium interacts with the clay particles, not affecting the crop but affecting the soil; and then there are the direct ion toxicity effects on the plant when there’s too much chloride or boron.

Dr. Hoffman determined that the second two types of effects really weren’t an issue in the southern Delta given the soil conditions and the constituents in the water, so the focus is really just on the first category of effects, Mr. Gowdy said.

Gowdy PlantThe evapotranspiration needs of a plant are satisfied by applying water to the soil, and that water is either precipitation which is salt free, or irrigation water, which can have varying amounts of salt, he said. The plant will uptake water by a process of osmosis, which is very similar to the process of reverse osmosis where clean water is extracted from salt water, where the plant takes the water and leaves the salt behind, he explained. The salts start to accumulate in the root zone and as it increases, the plant has to exert more energy to extract the water from the increasing gradually saltier water in the root zone, and by expending this energy, it takes away from energy to grow, stunting the growth of the plant, and ultimately affecting the yield, he said. The concentration of salt determines how much flushing of water is needed through the root zone, he said. “The more water you apply to the surface relative to the needs of the plant, the more water will drain through and flush soils out and reduce stress,” he said.

The term for this is called a leaching fraction, which refers to the amount of water that drains through and flushes through the soil column relative to the amount that’s applied, he said, explaining that a .2 leaching fraction would mean that 20% of the applied water is actually flushing through the root zone. That’s an important term in the calculations or the estimation of objectives, he said.

Gowdy Crop Salt ToleranceSome crops are more sensitive to salinity effects than others for a given amount of evapotranspiration, and salt concentrations, so we used DWR crops survey data from 1976, 1988, 1996, and 2007, and broke crops down by salt sensitivity, he said. “Out of roughly 100,000-110,000 acres of irrigated acres in the Delta, about 10% were salt sensitive, and these are crops such as dry beans, almonds, and walnuts. About 60% were moderately sensitive, and those include tomatoes, corn, alfalfa, squash and vineyards. There’s actually been a slight increase in the amount of salt sensitive and moderately sensitive crops over the 30 year period.”

In 2010, Dr. Hoffman reviewed the latest literature on the numerous factors, and then looked at the available data in the south Delta and evaluated whether or not any of these factors or whether they were controlling crop yields in the Delta with the osmotic stress factor being the main problem; sodicity and toxicity were not of much concern, Mr. Gowdy said.

Gowdy salinity 1Dr. Hoffman developed a steady state modeling approach to help determine protective objectives, he said, presenting a graph showing the results of dry bean yields versus salinity with a leaching factor of .20. He noted that the Y axis is relative yield and on the X axis, is the salinity concentration in the irrigation water. “What you see is you can have irrigation water salinity up to 1.4 deci-Seimens per meter (dS/m) before you reach a break point and start to see a decrease in yield,” he said, noting that the solid blue line is the calculation of that, assuming average precipitation amounts in the southern Delta.

However, if you have less precipitation and are relying more on irrigation water which contains salt, you would need to have less salt in the irrigation water in order to maintain concentrations below the impact threshold for, in this case, dry beans,” he said. “You can see