Fish in the Bay – November 2019, UC Davis Trawls – Blue Fish!

Happy Thanksgiving!

BE THANKFUL FOR THE RAIN.  Cool-season rains were long overdue when we trawled on 9-10 November.  The fish were few, and they were turning BLUE.  Read on.


Trawl map.


Bay-side station trawling results.


Upstream of Railroad Bridge.

FEW FISH!  89 on Saturday; 59 on Sunday!  This is the lowest monthly fish count I have recorded in over 3 or 4 years of counting.  I am inclined to attribute this fish deficit to high salinity and late Autumn rains:


But, trawl catches are highly variable.  These low November fish counts could be a result of bad luck as much as anything else.

I tabulated November fish counts from 2014 to 2019 against average surface salinity and temperature from discrete readings at the 20 LSB stations.*  As shown above, surface salinity was a bit higher on average than any other recent year.  However, only half the stations showed record-high salinity, the others were well within the previous 5-year ranges.

For commonly caught fish species, catches were all low but not record-breaking – with three exceptions:

  • Staghorn Sculpin. None were caught this month.  23 was the previous record-low for a November.
  • Starry Flounder. Only two were caught.  But, we have seen as few as 3 and 4 over the previous 5 Novembers.
  • Shimofuri Goby. We netted 23.  This was a record-high for a November!  These were all tiny Shimofuris that in past years would have been counted as “unidentified.”  And, I think we are witnessing a Shimo-explosion as discussed further below.
  • All other fish numbers were low, but not exceptional. Overall low abundances this month may have been simply a perfect fish-storm of random variability – I hope!

(* I only have salinity and temperature readings from 2016 on.  I also recognize that discrete surface readings are themselves highly variable and not always representative of general physical conditions.  Also, 2014 counts were from 5-minute trawls, so all raw fish numbers were doubled.)


Micah Bisson releasing lines on Saturday morning.  (Pat Crain at the helm.)


1. Hunting and Fishing Season – documenting Beneficial Use attainment.

Fall is Hunting and fishing season!  Beneficial Uses Attained in Lower Coyote Creek!

The California State Water Resources Control Board designates “Beneficial Uses” of water bodies throughout the state.  This concept goes back to the U.S. Clean Water Act of 1972, and earlier legislation, that set goals to make the nation’s waters “fishable and swimmable.”

To make a long regulatory story short, two Beneficial Uses designated for San Francisco Bay are: Water Contact Recreation (REC1) and Noncontact Water Recreation (REC2).

  1. REC1 includes: swimming, wading, water-skiing, skin and scuba diving, surfing, whitewater activities, fishing, and uses of natural hot springs.
  2. REC2 includes: picnicking, sunbathing, hiking, beachcombing, camping, boating, tide pool and marine life study, hunting, sightseeing, or aesthetic enjoyment.
  3. Other Beneficial Uses include: Fish migration (MIGR), Fish Spawning (SPWN), & Estuarine Habitat (EST), for example.
  4. Note: Convenient places to dispose trash (TRASH) or sewage (POOP) are NOT Beneficial Uses!


2. Longfin Smelt

Good News:  Longfins are returning for the 2019/20 spawn and half (2 of 4) were caught in restored ponds.

Bad News:  SF Bay Longfin populations are very low in late-2019, including here in Lower South Bay.


Longfin yearlings are returning to freshwater creek mouths to spawn.  Other anadromous fish, like salmon and steelhead do roughly the same.  We do not know to what extent Longfins seek their natal stream.  Ongoing UC Davis otolith studies should determine this soon.  But, we have learned a few things:

  • Since 2017, Alviso Marsh Complex & Lower Coyote Creek has been the most significant remaining Longfin spawning area in SF Bay.
  • The last few years of observation suggest that longfins assemble in lower downstream marshes in late fall. As waters cool and freshen up, males swim upstream to stake out prime spawning beds.  Females follow over subsequent days and weeks to deposit eggs.  So it seems …

Parasite!  The Cymothoid gill parasite is an isopod from the deep Bay or ocean. (See January Fish in the Bay report, “Parasite Paradise”  This isopod is another clue that this fish recently swam in from the deep Bay.


3. Baby Fish.

A variety of young gobies at Alv3

We continue to see a late-year surge in baby gobies.  Once again, many of these young gobies appear to be Shimofuri/Chameleons.  (The two types are indistinguishable when young.)


  • Shimofuri/Chameleon gobies have longitudinal stripes when young.
  • Shokihazes have alternating light and dark bands.


Young Shimo/Chameleon Gobies were again caught at stations ranging all along the Lower Coyote Creek system.  I continue to suspect we may be seeing a significant Shimofuri or Chameleon Goby explosion.


Baby Anchovies.  As in previous years, very young juvenile anchovies are showing up in late fall.  The larval forms are clear and colorless.  They “silver up” as they age.  Then, blue or green color begins to develop at the crown of the head as their bodies fill out.


It seems that dorsal color, either blue or green, never fully develops in Bay Anchovies.  I continue to presume that intense blue-backed and green-backed Anchovies develop their colors out at sea.


4. Unexpected Events

Saturday:  Line tangled in the winch at Coy2. Micah untangles.  Herons and seals watch. 

We experienced a few hiccups in November.  They slowed us down a bit.  Nothing serious.


Sunday:  A ripped net. Micah weaves.


5. Blue Fish

Blue American Shad.

American Shad.  Only 5 American Shad were caught.  But, these late fall returnees gave more good examples of color change in shad.  These two from LSB1 were the brightest and bluest we ever caught.

Anchovies, Shad, Herring, and Sardines are all distantly related as members of the Clupeiform Order.

I am guessing that dorsal color development in these Clupeiforms follows similar rules.  As mentioned last month …

  • American Shad seem to change color rapidly in response to salinity. I have found green and brown American Shad together at brackish salinity, but never a blue one upstream nor a brown one in the deep Bay.
  • Pacific Herring colors might change a little more slowly.
  • Northern Anchovy colors appear to change very slowly, if at all: I occasionally see bright blue or green Anchovies at far upstream stations. (But, as noted before, Anchovy colors apparently fade rapidly in the Bay even as the hue remains unchanged.)

Note:  I do not include Threadfin Shad in this scheme.  Threadfin dorsal color never seems to change appreciably.  It is always lavender-blue.  Threadfins also do not range out into the ocean, hence they are exposed to smaller salinity changes.


Same blue shad.  I took multiple photos because these fish dazzled all of us on the boat.  Even their iridescent silvery sides shimmered blue at the right angles.  (Have you ever seen such a beautiful fish?)


Green American Shad.

Further upstream in Pond A19 the following day, an American Shad had the characteristic brackish-water green hue.


Bronze American Shad

Again at the consistently freshest water station, Art1, this American Shad had a brownish-bronze back.

These observations help solidify the Clupeiform dorsal color hypothesis:

  1. Blue = high salinity.
  2. Green = mid-salinity.
  3. Brown/Bronze = fresh.


Bright blue anchovies at Coy4

Bright Blue Anchovies are most often caught at downstream stations like LSB1, LSB2, or Coy4.  And, bright color fades as the fish lingers in the Bay.


Faded blue Anchovies at Alv1 and Alv2.

Faded blue Anchovies.  These fish show faint blue chromatophores on the head and along the lateral line.  But, blue pigments are almost absent over the rest of the dorsal side.

Blue and greenish-blue Anchovies in Pond A21.

As discussed before, many blue-backs seem to take on a slightly warmer, greenish hue farther upstream.  I still suspect this might be a result of hybridization between blue-back and green-back lineages.  But, I am beginning to think that a blue-to-greenish color transition may occur at lower salinities.


Bay-hatched young-of-year Anchovies do not appear to develop much color.

  • They silver up on their sides, but backs and the posterior portion of the abdomen remain translucent.
  • What little color develops at the crown of the head and along the lateral line is generally blue for fish caught in the deep Bay (LSB stations).


However, Anchovies showing a green crown with blue lateral line are not uncommon.  … 

Wouldn’t it be interesting if the distribution of color could tell us what conditions this fish experienced as it recruited and aged, eg: green crown = low salinity at young age; blue lateral line develops from exposure to high salinity later in life??


More silvery-translucent Anchovies with blue to blue-green crowns from LSB.


Warmer greenish tones as we moved upstream to Pond A19.

Once again, Anchovies generally appeared more greenish at upstream stations.


But, there were also some young blue Anchovies in the same pond.  At least one had a green crown and blue back.

I suspect these Anchovies appear a little more bluish due to higher salinities this November.  Compare and contrast these photos with photos taken in September (

  • November anchovies are considerably bluer overall.
  • Golden-green, gold, and brown-back Anchovies that were common in September seem to be totally absent in November!
  • Did higher salinity turn our golden-green and brown-backed Anchovies blue?

Reminder – biologist Carl Hubbs reported that Northern Anchovies were brown-backed out to Sausalito and then green-backed beyond that point in 1925.  Has increased Bay salinity since then turned our brown-backs into green and blue-backs??  I’m asking for a friend.


Green Anchovy

Art2 is just downstream from the San Jose-Santa Clara Regional Wastewater Plant, The water is freshest and Anchovies are generally greener to brown here.


6. Comb Jellies usually correlate with high salinity and cool temps.

Ctenophores (Comb jellies).  Dozens of comb jellies were caught on the downstream side on Saturday.  These little jellies show up in Lower South Bay from time to time.  We usually see them in winter when LSB temperatures drop and salinity is high enough to approximate ocean conditions.

Four comb jellies were caught as far upstream as Alv3 and Coy2 which might be another sign of unusually high salinity.


7. Tricolors or “California Bicolors?”

Tricolored / Red-winged Blackbird update.  Once again Micah spotted our tiny flock of Tricolored or Red-winged blackbirds perched on bulrush along Dump Slough.  Lighting was not great.  And, once again I forgot to listen for …

Based on these, and last month’s photos, I have received split decisions from more experienced birders.  These birds could be either Tricolored or Red-winged (probably the California bicolor variant).  Tricolors are known to live in this area.  It could go either way.

According to “All About Birds,” female red-winged blackbirds (California bicolored variety) are more uniform brownish colored and have less streaking.

or, maybe not …

Given the misty lighting, I couldn’t determine the level of streaking for this female shown at right.  If this gaggle of blackbirds sticks around, Micah and I will listen for their call.


Once again, Happy Thanksgiving.  Rainy days are here again!

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