Fish in the Bay – 9 July 2017 UC Davis trawl – Green Water & Low DO

A July update on fish trawling…  I was out with Hobbs and the UC Davis crew on 9 July on the Artesian/Upper Coyote Creek side.

Dr. Diana Lin from San Francisco Estuary Institute (SFEI) rode along with us to collect fish samples for a triclosan study.  Levi Lewis, Pat Crain, and myself rounded out the crew with Jim Hobbs for a bright sunny day of trawling.

Jim Hobbs performing the invocation and ritual sacrifice.  Yes, Dr. Hobbs really sacrifices a sprinkle donut to the sea & marsh spirits each trip to ensure a safe and productive survey day.

Saturday – Bay side:

Sunday – Upstream side:

Earlier this year, intense rains in February freshened up the entire Lower South Bay.  The freshness is thought to have caused a shark die-off in parts of the Bay.  But, five leopard sharks were caught on Saturday, so sharks are still around!  The February Freshwater Flush of 2017 also stimulated Longfin Smelt spawning in Pond A21 that Dr. Hobbs documented in March.  July data shows that salinity has bounced back a bit but continues to be slightly lower than mid-summer norms at upstream locations.

Dissolved Oxygen (DO) was very low at all Sunday locations except immediately downstream of the San Jose/Santa Clara Regional Wastewater Facility.  DO usually drops in mid-to-late summer, but DO was low for a July.  I recorded top DO/bottom DO at several stations to give a better idea of the range of DO in the water column. (DO below 5.0 indicated in red.)


Greenness = Chlorophytes. Soon after launch, we all noticed that Artesian Slough water was very green.  Green color indicates presence of chlorophytes, or possibly euglenophytes, in addition to diatoms (Diatoms, by themselves are brown – they are related to brown algae.)  Just a little further downstream, we passed the Pond A16 discharge gate.  There we could see green water shushing out of the 243-acre pond.

Since 2005, roughly 1700 acres of former salt ponds have been breached for circulation close by along Artesian Slough and Lower Coyote Creek (not counting Ponds A6, A8, and A10 pond complexes further downstream). Fish and phytoplankton data appear to confirm that these ponds are acting as “giant green food producing machines.”

Pond A18 discharge structure on 7 May when vivid green water was oozing out.  Presumably this is chlorophyte-rich water that incubated in the shallow pond as it mixes with the browner more predominantly marine diatom Bay water. This is microbiology you can see with your naked eye!

I mapped green Xs near the two locations where “green water” photos were taken. 

The map shows Artesian Slough in relation to surrounding ponds. It is placed against a graph of phytoplankton data collected since early-2016.  Our own phytoplankton samples, collected at the yellow dot on the map above, show that diatoms (brick red) almost always dominate as biovolume, but chlorophytes (green) occasionally compete.  I would speculate about the influence of seasons, but our 13 months of survey work is still too limited.

Chlorophyll.  We have only three recent measurements of chlorophyll-a at Station SB13: 26 May – 42.5 ug/l, 1 June – 102 ug/l, and 23 June – 185 ug/l.  This is quite high.  Open Bay water typically has much lower chlorophyll – usually in the single digits and at times up to 10 to 20 ug/l or a little higher.  Hopefully, high chlorophyll at SB13 further confirms Dr. Senn’s hypothesis that shallow restored salt ponds are phyto factories feeding the system.

First Trawl – a Big Bag of Bass.  As Levi Lewis pulled up the first trawl we could see it was a big catch: 69 striped bass!  That is a lot of bass for a single trawl.  In fairness, much of the bulk in the bag was a bulrush rootball, but nonetheless, it was still a lot of fish.  Dr. Hobbs speculated that the bass may have been driven upstream by overall warm, low-DO conditions.  Elsewhere, bass would head to deeper, cooler, oxygen rich water in the Bay if they can find their way.

Typical Striped Bass from the big bag. 

Other fish from the big bag of bass.

A turkey vulture perched over a dead bass near the end of Artesian Slough:

Heat. Water temperatures were warm all weekend.  A week-long heat wave starting 19 June raised water temperatures to 24 to 25 degrees C, and water temps seem to be staying there. 25 degrees C is the life-threatening upper threshold for Striped Bass, and indeed, various observers reported sightings of dead striped bass over the past month. We saw only two dead striped bass on Sunday.


Invertebrates.  I added shrimp and Corbula data to the tables above to show distribution of a few of the more interesting invertebrates. Big numbers of shrimp and Corbula were observed on Saturday.  The invertebrate catch on Sunday was relatively meager.

A pair Palaemon shrimp females full of eggs.

Paleamon and Exopaeloman shrimp side-by-side to show the different rostrum shapes.  Exo’s tend to be clear bodied compared to darker tan Paleamon.  We didn’t see any native Crangon shrimp on Sunday.

Invasive Corbula clams.  Corbula populations haven’t exploded in Lower South Bay like they have in Suisun.  You can see on the chart that quite a few were collected in the trawl net nearer to Alviso Slough.  We don’t see so many further up Coyote Creek.

Corbulas can be disruptive pests.  I used to stomp on them on the boat deck, but it occurred to me that that could release larval clam veligers back to the Bay or something.  This time, I collected my Corbulas in a jar for more effective pickling and disposal.  We all have to do our part!  – also note the browner water color further up in Coyote Creek.

Yellowfin Gobies were the most common fish found both Saturday and Sunday: 385 of them were caught each day.  This is not great news.  Yellowfins are considered noxious invasive.  However, unlike Corbula, I let them live for no good reason.

Yellowfin Gobies caught eating the sticklebacks!  At first, I thought this pair below had party favors, or maybe they were sticking their tongues out at me.  Nope, they were swallowing a three-spined sticklebacks – additional evidence that yellowfin gobies exert pressure on larval and tiny fish populations.

Other gobids.  Native Prickly Sculpins were picked up at different stations each day.  The pricklys are continuing reminder of the February Freshwater Flush.  We had not been seeing them for the past few years.  They needed a good flush of stormwater to kick them out into the Bay.

Native Arrow Gobies are even tinier.  Only a few were caught each day.

Longjaw Mudsucker.  Dr. Diana Lynn marveling at one we caught.

Tule Perch. A single Tule Perch was collected at the UCOY 1 station.  This is only the second Tule Perch ever found by Hobbs in Lower South Bay, the first having been discovered on May 7th.  This is another sign that effects of the Freshwater Flush continue to linger – and a second indication that the Coyote Creek population of Tule Perch, once considered extinct, may be well recovered.


A19 Spartina and pickleweed. I noticed in April that the February Freshwater Flush appeared to cause a massive die-off of Spartina and Pickleweed on Pond A19 mudflat.  This was very dismaying. I had been photo documenting the marsh plant colonization since 2013.  I could also see that bird foraging almost ceased altogether which could indicate that benthic bugs, like corophium, got hammered by the freshness.

Pond A19 on 9 April.  Looking into the pond from the breach.  Gulls, coots, and little sign of vegetation. The mudflat was denuded!!!

Pond A19 on 7 May 2017:  Tiny shoots appear.

Pond A19 on 9 July: the Spartina bounced back from rootstock and was looking robust, but not quite as tall yet.

By 9 July shorebirds were again foraging, so I suppose benthic bugs reemerged.  A new broad leaf plant had spread over much of the mudflat but seemed to be desiccating as salinity increases.  I don’t know enough about marsh plant succession to describe in accurate terms, but, I am guessing that the freshwater die-off was only a temporary, possibly beneficial, phenomenon.  The plants are back!


Jim Ervin
Compliance Manager
San Jose-Santa Clara Regional Wastewater Facility


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