Fish in the Bay – December 2021: End of the first Dry La Nina Year.

2021 was a very good year in Lower South SF Bay (LSB) for most fishes.  Many records were broken, for better and for worse: 

  • Good Records: 2021 was our record year for Anchovies, Herring, English Sole, threatened Longfin Smelt, Leopard Sharks, Brown Smoothhounds, and Bat Rays.  We also caught more native Bay Gobies (33) and baby White Croakers (10) than we have seen in previous years.
  • Bad Records: 2021 also brought us record-breaking catches of non-native Shimofuri Gobies and Palaemon Shrimp. And, numbers were low for some native fishes, like Prickly Sculpin, California Halibut, California Tonguefish, Three-spined Stickleback, and Starry Flounder.
  • Worst of all: After June, it was a tragic year for native Crangon shrimp that depend on robust rainwater flushing. By this December, we should have seen at least hundreds of adult females brooded with eggs.  So far, we have found none!  Mysid blooms are also looking very weak. 


Pelagic fish collage: Northern Anchovies, American Shad, and Longfin Smelt, Dump Slough, December 5th.


“La Nina” cool ocean upwelling.  According to NOAA, the West Coast experienced the best ocean conditions for finfish production in 24 years.  We detected population booms in most species that spend parts of their lives in the ocean.

Extreme drought was another driver.  Prickly Sculpin, Sticklebacks, and Crangon Shrimp greatly depend on rainwater flushing for successful reproduction and recruitment.  2021 was a very bad year for them.        

Salt Pond Restoration is the wild card.  Many of the record numbers of native Anchovies, Longfin Smelt, Pacific Herring, Bay Gobies, and White Croakers were caught in restored former salt ponds A19 and A21. Trawl data indicates that these restored habitats have become preferred spawning and/or nursery habitats for these species.

  • Hopefully, the encouraging numbers continue to reflect long-term improvement!   


Northern Anchovy spawning season is over.  Despite a late-year surge in numbers, only two Anchovies appeared to be spawning-ready out of many checked in December.  The winter-time shift to cooler temperatures appears to trigger an abrupt end to Anchovy spawning in LSB.  

New Fish.  We caught two new visiting fish species:  a Red Irish Lord, and two Pacific Tomcods discussed farther below. 


Longfin Smelt spawning was detected in December. Longfins are triggered by low temperatures (degrees C in the mid to low teens).  After the drop in temperatures, over a hundred spawning-ready Longfin Smelt were caught in upstream marshes. These were the same stations where Anchovies were spawning only a few months earlier!  

White Sturgeon.  Two Sturgeon were viewed on sonar but not caught. 


1. Results from December Trawls – American Shad.  

American Shad from Pond A19.

American Shad.  Even though non-native, it is hard not to like the Shad.  They are highly edible and very attractive to look at.  And as far as we know, are not upsetting the ecological order here. 

Also, a correction.  Last month I wishfully speculated that American Shad might be returning here each late fall for spawning.  Actually, American Shad spawning has only been confirmed far north of here, in the main stem of the big Sacramento and American Rivers, in late spring (May-June). The smaller juveniles we catch in Coyote Creek are likely returning only for the food as far as we know.


2. Topsmelt

Topsmelt in Pond A21 on December 4th.

Topsmelt.  194 Topsmelt were caught in 2021.  This was our second-highest annual count after 2020.  Topsmelt stick close to the shallow water vegetation, especially when disturbed.  For that reason, we usually catch very few of them despite their local abundance. 

Until this year, mid-sized adults, like those shown above, have always been quite rare for us. Adults tend to shun fresher water. The larger number of adult Topsmelt could be attributed to lack of rain and saltier conditions.  … Or, perhaps Topsmelt are simply doing better this year.


 3. Anchovies!

Northern Anchovies and Palaemon Shrimp at Alv3 on 4 December.

Northern Anchovies.  The December Anchovy count was 1,556.  We have grown to expect adults to flee from LSB as temperature drops in winter.  It doesn’t always happen, and it did not happen this year.  Instead, we were up to our elbows in adult Anchovies along with many young recruits. We counted more adult Anchovies in December than any other month in 2021. 

Did we again just witness a wintertime migration of coast-based Anchovies into the Bay?  Many of these fish look suspiciously long and skinny.


Side-by-side comparison at Coy3: Long skinny Anchovy from the cool ocean (top).
Stubby, full-bodied Anchovy from the warm Bay (bottom).

Bay/estuarine-raised Anchovies grow fast in warmer water.  But, they also cease growing earlier in life. In his 1925 paper, biologist Carl Hubbs counted one or two fewer vertebrae and shorter lengths in Anchovies, Herring, and Sardines raised in warmer waters compared to those raised in cooler temperatures along the California coast. 

Someday, we could verify and further refine Hubbs’ Anchovy growth hypotheses.  Unfortunately, this would require sacrifice of a few fish to count vertebrae and analyze otolith ear stones.  For the time being, we merely photograph and release each one.  


Another long skinny Anchovy at Coy4


The last two spawning Anchovies of 2021.  Interestingly, the only two spawning-ready Anchovies observed in December were short and stubby.  Generally speaking the vast majority of spawning anchovies in summer are also shorter and full-bodied.  This seems to suggest that Bay-raised Anchovies make up the majority of summer-time spawners.


Baby Anchovies!  The tiny ones shown above are new baby recruits from the previous summer-fall spawn.  The 2021 anchovy spawning season appears to have been a success!  

(Note:  Our coarse otter trawling net is not optimized for collecting larval Anchovies. Most babies slip through the net.)

Big Mama Anchovies.  At least once every month or so, we find a few monster Anchovies measuring 110 to 135 mm.  Anchovies of this length are likely 4 or 5 years old.  They seem to arrive somewhat randomly throughout the seasons.  Where do these jumbo Anchovies live and feed when not in LSB???


Bigger Anchovies at Art2.

Anchovy size gradient.  Average Anchovy sizes and ages are always smaller at LSB stations: none were over 80 mm in December.  The largest Anchovies are found in upstream ponds and sloughs: several were over 80 mm, none smaller than 50mm, and only two less than 60 mm at upstream stations in December. 

The trend is clear, big Anchovies migrate as far upstream as they can!  But, why do they continue to do this after spawning season has ended?  What are they eating?


4. Staghorn Sculpin.

Staghorn Sculpin adults continue to arrive for their spawn.  56 were caught in December.  This is our highest Staghorn December since 2012.  However, no clear signs of egg-bearing females or mating-ready males have yet been observed. Staghorn babies usually start showing up by January with peak recruitment around March.


5. Speckled Sanddabs.

Speckled Sanddabs.  11 more sanddabs were caught in December to bring the 2021 count to 60.  This was a very good year, but still short of the record in 2016.

BTW, we usually catch babies of the smaller “Speckled” Sanddab variety. These are edible, but those caught and eaten on the coast are mostly the slightly larger “Pacific Sanddab.”   


6. English Sole.

This was the first and only English Sole caught for the 21/22 season.  As usual, this fish was infected with the protozoan “X-cell disease.”  If luck and cool upwelling holds, we should see over 1,000 English Sole by March. 


7. Shrimp Wars.

Palaemon Shrimp (top) and two Crangon (bottom) at UCoy1.

Crangon Shrimp.  289 Crangon were counted in December as opposed to almost 4,700 Palaemon non-natives. 

  • Good news: This is the most Crangon we have seen since June. 
  • Bad news: This is still a crushingly low count for a December.
  • More importantly no pregnant females bearing eggs have been observed! We should be seeing hundreds of berried females by now.



A mysid at Art1

Mysids.  Mysid counts have been low all year.  By this time in a good wet flushing year, our net would be clogged with them.  Mysids are highly desirable food for fish. 

One wonders what all the fishes are eating right now since mysids are scarce. …    Or, are mysids now rare because all the record numbers of fishes are eating them?


8. Two New Fishes in December!

Red Irish Lord – A new fish in South San Francisco Bay.  We caught this strange bottom-dweller far out in LSB.  In 10 years of trawling, we had never seen one like it.  It was obviously some kind of Sculpin or Scorpionfish.  The pinkish hue, reminiscent of coralline algae, indicated that this one belongs in a California coastal tide pool but not in South San Francisco Bay.


We were temporarily stumped on its identity.  But, according to “the book” (Miller and Lea’s Guide to the Coastal Marine Fishes of California), this little guy, or gal, is a “Red Irish Lord.  Irish Lords come in red, brown, and yellow varieties and live up to six years and grow to between 12 to 20 inches.


Pacific Tomcod.  Tomcods are another common coastal fish. Growing to roughly 12 inches max, they are the smallest members of the bottom-dwelling “Cod family,” aka Gadidae.  Other family members include Cod, Pollock and Hake. 

  • Members of this family have three dorsal fins, two anal fins, and usually a single whisker-like barbel under the chin.
  • Schools of Tomcod forage over sandy or rocky off-shore ocean bottoms out to several hundred meters deep.


9. Odd Critters!

Philine egg sacs, aka “Boogers.”  We continue to count Philine headshield sea slugs.  But, now that we know that “jelly fragments” are really Philine egg sacs, we may drop “boogers” from monthly counts altogether. 

  • The monthly number of egg sacs is often high and their geographic dispersion is wide.
  • Each egg sac contains many thousands of near-microscopic eggs. Counting these sacs is unlikely to generate any useful information.

“Devil Bugs,” aka Cymothoid Isopods.  Devil bugs are important gill parasites that infest many fishes that migrate from the ocean.  Their numbers are surging as Smelt, Shad, Herring, and (now) Tomcod return.  Bad parasites can disrupt ecosystems.  We keep an eye on these bugs. 


UCoy2 Anemone planted on a Corbula at UCoy2.

Orange-striped Anemones.  Like egg sacs and devil bugs, Anemone numbers are always partial counts at best.  The largest of these tiny orange blobs measure 1 cm at most, and they are easily missed in piles of shell hash. 

In previous years, we found them only on ancient oyster shells at deep Bay stations.  In 2021, their range spread far upstream with specimens being found at practically every station.  They must cause some impact in the upstream ecosystem.


10. Birds.

Great Blue Heron fishing in Pond A21 at high tide.


American White Pelicans soaring over Coyote Creek at UCoy1


Surf Scoters loafing near stations LSB1 and LSB2 in December.

Comments are closed.

%d bloggers like this: