Fish in the Bay – November 2021: Winter Fish Transition.

Happy New Year 2022.

I am thinking about 2021 in review, but at the same time, I am still catching up with on reporting early November trawls. 

Overall, 2021 began with a very encouraging population boom of Crangon Shrimp and baby Anchovies.  Then, we experienced population explosions of young Staghorn Sculpin, Pacific Herring, and English Sole that is probably attributable to La Nina cool upwelling off the coast.

The near rainless winter and spring of 2021 made the Bay very salty. Plants and creatures became increasingly marine.  Crangon Shrimp populations totally crashed and were replaced by Palaemon after June. Much of LSB got covered by slimy Ceramium red algae sprinkled with tiny anemones and nudibranchs.  Then, non-native Inland Silverside and Shimofuri Goby populations boomed in late summer. Aside from the best Bat Ray and Leopard Shark pupping season we have ever seen, the situation was rather depressing by September and October. 

But, only one or two Atmospheric Rivers can make a huge difference here:  A big bomb cyclone hit us on 24-26 October – 

Just a few weeks later, some changes were seen in November trawl results.


Bay-side stations trawling results.

The bomb cyclone caused a slight drop in salinity at upstream stations, however, temperature and dissolved oxygen parameters were largely unchanged from November.  Nonetheless, the fishes know when it’s time to move.

Summer Fishes Decline:

  • There was a huge reduction in nuisance non-native Inland Silversides and Shimofuri Gobies. (This is the best news from November. We were in extreme danger of being swamped by these invaders.  The fish world in Lower South Bay is safe again, for now…)
  • The Anchovy count dropped from 456 to 143.


Upstream of Railroad Bridge.

Winter Fishes Arrive:

  • American Shad started to show up: 26 were caught in November, up from one in October.
  • Staghorn Sculpin returned for their spawn: numbers increased from 54 to 138.
  • Two White Sturgeon were spotted on Sonar near UCoy stations. And, we examined a dead Sturgeon in Dump Slough – more on that below.
  • Longfin Smelt count dropped to 25 from 37 in October. This was disappointing but not alarming.


1. Staghorn Sculpin.

36 Staghorn Sculpins were caught at Alv2 alone!

Staghorn Sculpins are seen throughout the year.  In good years, their numbers peak around April when we catch dozens to thousands of babies in the trawls. 

On paper, their numbers drop around November through February.  But, that is a bit deceptive.  The smaller number of Sculpins we see in the cold months are almost all big fat adults returning to spawn.  (‘Big’ is relative here.  Staghorn Sculpins grow much larger on the coast!  Our Sculpins tend to be midgets in comparison.)


Four Sculpins at Art3

Very soon now, male Staghorns will hunker down in mating caves.  They attract females to deposit eggs.  Then, the males guard the eggs for weeks without emerging.  


White splotches on a Male Sculpin’s head?  Pond A19

In winter, Staghorn Sculpins with white marks on the head and over the eyes are occasionally seen.  We suspect that these are the males.  White splotches may be used for territorial display.  Literature seems to be silent on this issue.  We continue to monitor. 


2. American Shad.

Large and small American Shad, a Top Smelt (far right) and an Anchovy (bottom).  Dmp1

American Shad are another of our classic winter-time fishes.  They reliably return to the creek mouths in fall.  We consistently catch the highest numbers near November through perhaps March.  They must be spawning upstream here.  We have no hard physical evidence… but, why else would at least 2 or 3 year-classes of Shad return every year?    


More American Shad at UCoy1 on November 7th.

Shad are East Coast natives that became naturalized fish citizens in West Coast rivers over a century ago.  They don’t appear to impact other native species, albeit there is some concern that Shad may consume tiny food that used to support native Salmon populations.


3. Longfin Smelt.

Two young and scrawny-looking Longfin Smelt in Pond A21 on 6 November.

We only caught 25 scrawny and mostly young-of-year Longfins in November.  It was still very early in Longfin Smelt Season, nonetheless, the low number was a bit of a concern.  If Longfins cease spawning here, their future in SF Bay is bleak.

But, DO NOT BE ALARMED:  As reported in “Fish in the Bay, Longfin Alert” a few weeks ago, Longfin numbers sharply increased in subsequent December trawls.  Many larger/older spawning-ready fish were observed. They still have a chance!  



More young Longfin Smelt at Coy3

Since 2017, UC Davis researchers have identified spawning Longfins and fry in upstream Coyote Creek, Pond A19, and Alviso, Artesian, and Dump Sloughs.  This area is a critical spawning zone for these fish. It is also the most reliable place in SF Bay where spawning-ready Longfins are being collected each year to develop a lab-reared broodstock as a last best option.  


4. Speckled Sanddab.

Speckled Sanddabs spawn farther out in the deep Bay or at sea.  Very young fry swim upstream to feed and grow near the creek mouths.  They are always more plentiful here in the cooler months.  We caught seven tiny baby Sanddabs in November.  2021 has been a good Sanddab year with 53 caught so far.  

The 10-year Sanddab record has been very spotty: it ranges from only one (1) caught in 2018 to as many as 200 in 2016.  They seem to be rebounding each year since 2018.


5. Starry Flounder.


Starry Flounder and Longfin Smelt at Coy2 on 7 November.

Starry Flounder.  Nine more Starries were caught in November.  The year-to-date count is 64. In a great year, like 2012, 2016, or 2017, we would expect to see a few hundred by now.    

Starry Flounder and Diamond Turbot are exceptions to the ‘Flatfish Spawning Rule.’  Unlike Halibut, Sole, and Sanddabs that spawn out at sea, Starries and Turbots swim upstream to spawn in bays or creeks.  Starries spawn farthest upstream with the young migrating downstream after hatch.


6. White Sturgeon.

Dead White Sturgeon encountered in Dump Slough.

White Sturgeon.  Two Sturgeon were viewed on sonar as we cruised up the main stem of Coyote Creek on Sunday.   Then, we found this dead one measuring 1.35 meters in Dump Slough: cause of death unknown.  A physical examination was conducted and a fin ray sample was collected for determination of age.  The carcass was left in place to reassimilate back into the carbon pool.


7. Shrimp Wars.

Shrimp.  The ratio of non-native Palaemon to native Crangon Shrimp was roughly 100:1.  (Another 127 non-native Exopalaemon shrimp were caught mainly in Dump and UCoy sloughs.) 

Hopefully, egg-bearing female Crangons will show up very soon for their brooding migration.  So far, the Crangon outlook remains fragile and depressing.  … Let’s move on.


8. Sharks and Rays.

Young female Leopard Shark at LSB1

Leopard Sharks.  Our 2021 cohort of Leopard Shark babies are growing up!  They had many Palaemon shrimp to feed on this year.


A few shark Parasites at LSB1

Caligidae Copepod Parasites.  We picked these parasites off the big shark for close examination. The darker ones may be Achtheinus oblongus. The lighter-colored copepod on the right lacks the long tails of egg strings.  It is either younger, male, or possibly a different species altogether.


A total of eight Leopard Sharks were caught and released in November.  The year-to-date count is 54, a record-breaker! 

  • The three Caligidae parasites shown on the right have a distinctly greenish hue that we have seen before. Do these represent a different species of copepod?  Or, are they just younger? 
  • The sharks were released. The parasites were collected.


Brown Smoothhound.  Two Smoothhounds were caught in November.  The count is now nine for the year.  These small sharks (aka dogfish) continue to be heavily infested with parasites. 


Mid-sized Bat Ray at LSB1

Bat Rays.  The 11 Bat Rays caught in November increased the 2021 count to 130.  That is another 10-year record-breaker.  It was a record year for all three elasmobranchs: Leopard Sharks, Brown Smoothhounds, and Bat Rays.    

The lack of rain and increased saltiness encourages them to swim farther into Lower South Bay and upstream into the sloughs.  Shark and Ray abundance also correlates loosely with shrimp abundance.  Despite the mid-year crash in native Crangon shrimp, non-native Palaemon shrimp have been super-abundant.


9. Polychaete.

Nereid Polychaete Worm.  This is at least the third long skinny Nereid polychaete worm we picked up at LSB stations in 2021.  Each specimen was almost exactly 3 cm long.  What species is this?

  • The Nereididae family of marine polychaetes includes 500 species and 42 genera, so there are many possibilities.


 10. Bay Pipefish.

Male Bay Pipefish, Pond A21

Male Bay Pipefish with flaps open.  I have often wondered how male pipefish accept eggs from females.  Apparently, the male’s belly flap opens wide and the female deposits eggs that attach in two rows on each side.  (I think it’s around 20 or so on each side.) The male then closes the flaps tight into a belly brooding pouch. The dad unzips the pouch around 10 to 20 days later and the babies swim free.


Another Pipefish at Art3


11. Shimofuri & Chameleon Gobies.

A mixture of sick-looking Shimofuri & healthy Chameleon Gobies at LSB1

Shimofuri Goby numbers dropped from 997 in October to 483 in November. The vast majority of the decrease was from Station Alv1 in Alviso Slough alone. … Meanwhile, 54 Shimos were caught at station LSB1.   Late October bomb cyclone rains must have flushed them farther downstream.

Literature states that Shimos avoid salinities much above mid-20s ppt.  These Shimos at LSB1 looked sickly; their skins were pale and milky, their colors were muted.  I don’t think they swam here willingly. Could rainwater flushing have pushed them here? 


The Deep Bay is usually Chameleon Goby territory, but even they range upstream when salinity is high.  As mentioned many times, Chameleon Gobies are adapted to marine salinity and are close cousins of the Shimos.  Chameleon and Shimo populations frequently overlap.  It takes experience and some degree of luck to distinguish the two in the field. 


Healthy-looking Shimos in the fresher waters of Artesian Slough.

Reminder:  Shimofuri Gobies have orange margins on the anal and second dorsal fins, and have many tiny spots under the chin. 

  • Shimo and Chameleon body shapes differ as well. This is easy to see in photos but much harder to see in casual observation.


12. Anchovies!

Golden Anchovies from Artesian Slough.

Northern Anchovies.  The Anchovy count usually drops as temperatures cool and rains return in fall.  Last year, the Anchovy spawning season abruptly ceased after the first cold-snap in late October.  This year, 5 or 6 milt and egg-bearing adults were still detected in November.  Regardless, the apparent change in spawning readiness was still almost equally abrupt: practically every fish showed conspicuous signs of eggs or milt through the warm months of 2021, then suddenly by November, practically none of them did. 


The rainbow of Anchovy colors in Dump Slough.

Recent rain helped freshen the waters in some of the upstream sloughs.  More of the remaining Anchovies ‘browned-down’ to gold as a result.


Bluer/Greener Anchovies in Coyote Creek.

The mixture of blue, green, and golden Anchovies is always confounding.  


13. Ducks.

Ducks were present in restored ponds in November, but we could never get close.  It was hunting season, so the ducks were quick to flee as we approached – even from great distance.  Green-winged teal were easy to identify when the Sun was behind us.  Northern Shovelers were also conspicuous.  With difficulty, we spotted some Gadwalls and Widgeon. 

We need more ducks here!


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