Heron’s Head Salt Marsh Losing Salt


Actually, as it turns out, most of San Francisco Bay is becoming less salty these days.

Matteo Neivert, Exploratorium Visiting Artist, and I were hiking around the Heron’s Head salt marsh on Thursday morning of April 6th. I took several samples near our previous sampling sites, and while I was at it, I checked the salinity.

Matteo holding a sample.

Mateo holding a sample

A little background is in order. Average seawater is ~3.5-percent salts, mostly sodium chloride “table salt”, with a few other salts thrown in. Using an ordinary “wine country” refractometer, calibrated against deionized water, I usually read between 3.0% and 3.5%, depending on the location, for San Francisco Bay. Water in a slough or in salt marsh ponds is frequently 5% and may be higher in the late summer when evaporation concentrates the salts.

Heron’s Head is a tidal salt marsh. Much of the salt marsh is well under water from the Bay at high tide; and, as much as 2-feet above the tide level at low tide. Last November 13th, water from my usual sampling site on Heron’s Head tested 3.6% at mid-afternoon low tide. At 8:55AM that morning, at high tide, the sampling site had been about 3-feet under water. What this means is that Bay water resets the salt content of a tidal salt marsh pond every high tide.

I was startled when water from a pond well above my usual sampling site, so not well-washed by the tide, tested at 2.5%. I was even more startled when testing at the usual sample site showed a very low 2.2%, the same value I got when I sampled the Bay water in India Basin. I had not brought any deionized water to recalibrate the refractometer, so I was undertain whether these measures were correct.

When I got home I recalibrated the refractometer against deionized water, finding it just slightly on the high side of zero. I had expected an error on the low side, not on the high side…! Checking my samples showed an actual value of 2% for both the India Basin water and my usual sample site.

This indicates a very high seasonal run-off from the rain around the Bay, as well as rain falling into the Bay. High tide brings in a huge quantity of sea water from the near-shore Pacific ocean, so the dilution from fresh water running into and falling on the Bay must be substantial for the average salinity value to fall by more than 1%.

Later this week I will return to Heron’s Head for repeat measurements, carrying my deionized water for a standard to “zero” the refractometer against. If the weather permits, I will take the kayak and also check the salinity of water out towards the middle of the Bay.

I will also be looking at the Salt Marsh micro-community in more detail. I only took one quick sample from my usual sample site, but the usual well-ordered micro-community seemed disturbed when I examined it under the microscope.

Usually there is a well-defined “blue-green” top layer dominated by large Oscillatoria-like cyanobacteria forming a mat, with many diatoms. Any filamentous algae floats well above that layer. Below that layer is a thin layer of Beggatoa, a motil Archiabacterium that require both some sunlight and sulfides. Below the Beggatoa layer is black, sulfur-rich mud. This time, I found the cyanobacterial mat disrupted, with fewer cyanobacteria and both Beggatoa and filamentous algae mixed in.

Smaller cyanobacterium and diatoms

Another common diatom

In addition, I found large amounts of Melosira, a filamentous diatom.

Melosira sp.
Melosira sp.

Melosira sp. at higher magnification
Melosira sp. at higher magnification

Milosira and Green Filamentous Algae
Melosira sp. and filamentous green algae

This disturbed pattern of micro-communities may have been a sampling artifact. Only further study will make this clear. The presence of large amounts of Melosira, however, is unusual. I have found large mats of Melosira growing on boat-dock piers, but not in a salt marsh like this one.

4 Responses to “Heron’s Head Salt Marsh Losing Salt”


    I went back out this Friday afternoon. It was shortly after a moderate high tide. Both the Bay water in India Basin and the regular site pond water showed 1.8% at 18.3-degC. This is even lower than measured the first time. Usually layer of growth over the mud is either red or blue green. This time it was yellow. Previously this layer has been well defined and more like a mat. This time it was loose, breaking apart upon the touch. Examination of samples of the unconsolidated layer at 400X magnification show a loose collection of golden diatoms, with few cyanobacteria. Previous samples showed a dense mat of cyanobacteria with diatoms mixed in the mat. The Salt Marsh really is losing salt and it does seem to have changed the integrity of one or more of the communities. I am continuing this examination and when material is ready, I will post another discussion, comparing pictures from last fall with pictures from recent samples.

  2. Cris Says:

    It is great to hear microbiological news of Herons Head!

    I found an interesting paper of SF Bay Salinity from the USGS. They present seasonal data for the South Bay that seems to align well with your field observations. Their data are from 1993 and are difficult to read because the graph co-mingles observed with simulated. Check out:


    I came away from my quick read without an impression of the depth of sampling. I recall that there is also a vertical salinity gradient in the Bay during the spring season with lower salinities toward the surface.

    Another paper in EOS, the American Geophysical Union transactions, provides a somewhat tangential but entertaining account of Bay water salinity over a 400-year period. This history of salinity was developed by examining tree ring patterns in extremely moisture-stressed blue oak trees.


    Finally, I found a paper in Sweden (without much information to support a citation) that includes an interesting table of South Bay salinities by season (Table 3). The table shows winter salinities dropping considerably during ‘wet’ years.




    NOTE ON UNITS: The USGS folks start with “parts per thousand” to define “practical salinity units”. One part per thousand = 1/1000 = 0.001 = 0.1-percent by weight. So 33-parts per thousand = 3.3% “sea salt” by weight = 3.3-psu, which is a sort of average California coastal sea water.

    My measurements, mostly in the northern coastal waters, run slightly higher, 3.3% to 3.5%. This is probably the result of the Alaska cold current being near shore up here.

    My measurement of 2% salinity in the Bay and in the sample pond last week = 20-parts per thousand. If I weigh out a 1,000-g sample of that 2% water, how much is original sea water and how much is “pure” run-off?

    Remember, this is all by weight, so a 1,000-g sample contains 20-g of salt and 980-g of water. If the Bay was equilibrated with average coastal water, every 1,000-g sample would contain 33-g of salt and 967-g water.

    Well, if I added 1,000-g of pure water to 1,000-g of coastal water, getting a total of 2,000-g, then mixed it thoroughly and weighed out 1,000-g of that solution, I would only have 16.6-g of salt, or half as much salt, assuming the salt mixes uniformly and is divided uniformly when I weigh out 1,000-g.

    This tells us how to calculate the amount of run-off. In coastal water being diluted by X-g of pure run-off water, 33/[33+967+X] has to equal 20/[20+980] to get the value I measured. This equation reduces to 33/[1,000+X] = 20/1,000. That resolves to 33,000 = 20,000 + 20X, or X = [33,000-20,000]/20 = 650-g of pure water. So the 2% water I measured in the Bay and in the sample pond was 650-parts/1,000 = 65% run off.

    Although this seems to suggest that almost two-thirds of the water in the entire Bay is run-off from rivers, streams, and rain, it probably really means that only the top layer of water has that much fresh-water run-off. The USGS folks suggest this, noting that run-off and tidal mixing occurs mostly in the top layers of the water, with the deeper Bay water remaining more static.

    They also observe that most of the dilution actually comes from the river network flowing into the Sacramento River, then into the Bay. This is actually an enormous run-off catchment area, and includes the massive snow melt in the Sierra mountains.

  4. Cris Says:

    Hi Wayne,

    It occurs to me that, in the photograph above, Mateo is standing in the exact site where I collected the sample containing the interesting, highly-motile, as-yet-unidentified ciliates this winter (see January post Heron’s Head Critters). I have a folder of movies taken through the microscope while I was chasing the little guys around. Would you be interested in seeing these images of a late January sample?