Snapshots of San Francisco Bay’s ecosystem nutrition

San Francisco Bay: deeper than it looks

When you think of San Francisco Bay’s chemical patterns (you do think about the Bay’s chemical patterns, don’t you?!), it’s important to consider not just differences from the Delta down to the Lower South Bay nor just those from Oakland to the Peninsula, but also those from the surface to the bottom. In this second issue of The Mooring Report, we’re going to show some data that demonstrate how much just a few meters can matter in terms of chemical variability and why that matters for fish, birds, and humans.

Nowhere to hide

Why should we care about chemical variability as a function of depth?

Imagine you’re a fish and you need a certain amount of oxygen to survive. If oxygen concentrations are the same across all depths, that’s just great; you can hide wherever you want and focus on eating the rest of the time (what else is there for a fish to do, after all?). But if there is a large gradient in oxygen from the surface to the bottom, then you might have to come out of hiding—or even worse: close to the surface—to get that gulp of oxygen you need to survive. Now you’re a prime target for one of the many seabirds sitting on a pier piling. Have you ever looked at the Bay and not seen a few pelicans waiting for dinner?

We don’t know the exact magnitude of the effect of dissolved oxygen gradients on habitat quality in SFBay, but understanding vertical structure is a critical step toward figuring it out. Dissolved oxygen also has a large impact on benthic (bottom) creatures and processes. Ultimately, we hope to be able to estimate the total volume of low dissolved oxygen waters across the bay in order to determine how much of the variability is natural and how much is anthropogenic. There is no shortage of motivation to study the vertical structure of oxygen in SFBay!

Birds profile Alviso slough.


Drivers of vertical oxygen variability

There are a few different factors that can cause vertical gradients to set up in chemical concentrations; we’ll focus mostly on vertical variability of dissolved oxygen here.

  • First, oxygen is a soluble gas, meaning that it is constantly dissolving from the atmosphere into the water and coming out of solution from the water into the air. Which of those two processes dominates is determined by the water’s oxygen concentration: if the concentration is less than oxygen’s saturation in water, more oxygen will go into the water; if the concentration is greater than oxygen’s saturation value, oxygen will predominantly exit the water.
  • Second, oxygen is produced by microscopic plants in the water known as phytoplankton and macroscopic plants like seagrasses. So oxygen concentrations will be greatest where concentrations of phytoplankton are greatest which tends to be in shallower water where they can get enough sunlight.
  • Third, things that consume phytoplankton or other organic matter (like zooplankton, larger animals, and some bacteria) also use oxygen in the process. Frequently oxygen consumption is greatest near the bottom or even in the sediments due to the abundance of oxygen-consumers and general lack of oxygen-producers down there.
  • Fourth, in addition to these chemical and biological processes, physics gets into the picture and quickly makes things way more complicated. Currents can act to stir up the water and make it more homogeneous, but they can also carry water with distinct signatures from one place to another so that just measuring the chemistry but not knowing where that water came from can leave you very confused. It’s also possible to have fresh, lighter water (for example, from recent rain or melting snow in the mountains) flowing over top of saltier water, with minimal mixing between those layers. Now you can have two layers of water with fairly distinct physical, biological, and chemical signatures at one given spot in the Bay.
  • Lastly, humans can directly or indirectly influence all of these factors: warmer air and water means lower oxygen solubility; excess nutrients can cause large phytoplankton blooms and the oxygen consumption following their inevitable die-offs; and altered freshwater inputs (from stormwater sewers, wastewater inputs, etc.) can change physical circulation.
A few of the processes driving variability in dissolved oxygen. Red represents lower dissolved oxygen.


What do these patterns look like?

All of these processes conspire to create some very interesting patterns in dissolved oxygen as you go from the surface to the bottom. They also make it more difficult to study. We have moored, static sensors at eight locations (shown in map below), each at a set distance above the bottom. For an example of spatial heterogeneity ignoring the effects of depth for the moment, take a look at the dissolved oxygen time-series from moored sensors at Dumbarton Bridge, Coyote Creek, and Alviso Slough.

Dissolved oxygen at Dumbarton Bridge (DMB), Coyote Creek (COY), and Alviso Slough (ALV) and the depth record at Dumbarton.


Our moored sensor program gives us a great understanding of variability from one location to another but little idea of the vertical structure at any of those locations. To alleviate this data gap, we’ve done several “profiling” trips where we drive up and down the sloughs and lower a sensor over the side of our boat from the water’s surface down to the bottom repeatedly over the full length of the slough. This method, repeated at different tidal stages, allows us to get a much better picture of changes across multiple dimensions.

Here are results from a trip late last summer where we profiled along Alviso Slough at four different tidal stages. Take a close look at changes along the main channel, from top to bottom, and from one tidal stage to the next. Imagine what that variability might mean for fish living in that area.

Contour plots showing sections of dissolved oxygen in Alviso Slough. Along-slough distance ranges from 0 - 7 km, representing roughly 1 km upstream of the Alviso Slough EXO2 sensor (blue icon) to roughly 6 km downstream, where Alviso Slough meets Coyote Creek. Figures are arranged according to time/tide in a clockwise pattern.


Where are our sensors?

Each monitoring location in our sensor network was carefully selected in order to capture a unique influence or set of influences. Our sensors lie along the deep channel of the bay as well as in multiple shallower creeks and sloughs. SFEI’s Lower South Bay sensors are situated at the following sites (zoom, pan, and click icons for site names). Translucent blue circles represent profile locations for this field study:

EnViz: SFEI’s latest tool for visualizing water quality sensor data

Lastly, we’re continually updating our high frequency water quality data visualization tool, EnViz, both with the latest data and with new features to make it more user friendly. Visit EnViz in order to examine the above time-series and datasets including many water quality parameters, from temperature and conductivity to chlorophyll fluorescence and dissolved oxygen, across the Bay–Delta region.

Let us know if you find any interesting features in the data; we’d love to hear from you. What other types of figures would you like to see? What other analyses should we consider? What interesting features do you see in the dataset? Contact info is at the bottom of this email as is a link to additional San Francisco Bay water quality datasets.

Thanks for reading!

The Nutrients Team
San Francisco Estuary Institute

*Note: data have gone through a preliminary QC process but should not be published in their current format.
Email The Mooring Report’s editor, Phil Bresnahan, with any questions and comments.