Fish in the Bay – December 2023 – Merry Fishmas!

This is a pelagic fish holiday special.

Longfin Smelt and Pacific Herring have arrived in preparation for mid-winter spawning.  Young Shad and Anchovies also populate the cool-season fish gathering.

‘Silver fish, Silver fish, it’s Fishmas time in the marshes …”
(Sung to the tune of “Silver Bells” 

Bob Hope & Marilyn Maxwell in “The Lemon Drop Kid” (1951)


Fish counts at upstream stations.


Fish counts at downstream stations.


1. Longfin Smelt – a new record year!

Longfin Smelt count = 204.  We caught a lot more Longfins in December 2022, but this is still the second-best December catch in over 10 years of trawling. 

2023 is our new RECORD LONGFIN YEAR.  2,623 Longfins were netted in monthly otter trawls this year.  Prior to 2018, just 200 Longfins would have set a new record!   

  • This is a Fishmas miracle!


2. Colorful Clupeiform Fishes.

The Clupeiform family of fishes is mostly comprised of Anchovies, Herring, Sardines, Shad, and Sprats.  They are silvery pelagic fishes that mainly feed on tiny plankton.  

  • This Clupeiform group includes many of the most important forage and food fishes in the world. 
  • Herring and Shad spend parts of their lives in coastal waters. They return to the San Francisco Estuary each winter to spawn.
  • Anchovies migrate into SF Bay marshes to spawn in summer. Anchovies that hatch and rear in the Bay seem to become entrained as near year-round residents. They ultimately form a subspecies separate from the coastal population.


This December arrival of Herring and Shad presents yet another excellent opportunity to study Clupeiform color-changing characteristics.

Long-time readers of this blog will recall that the dorsal sides of Clupeiform fishes ‘Blue-up’ in high salinity above roughly 18 parts per thousand (ppt) and ‘Brown-down’ in fresher water below about 14 ppt.

  • This series of photo collages documents Clupeiform color performance over the 2-3 December weekend.

Stratification was high throughout the weekend; surface (top) salinity was several ppt lower than bottom salinity at several stations. 

  • Stratification is usually more pronounced during neap tides that coincide with quarter moons every other week.
  • Clupeiform dorsal colors generally correspond with lower surface (top) salinity because we fill our holding tub using surface water.


Pacific Herring count = 66.  Herring are now arriving for the winter spawn.  All of the Herring caught so far are small young-of-year, between roughly 60 to 75 mm standard length. 

  • Herring are very energetic swimmers, so our otter trawls likely tend to catch smaller, slower ones.


2023 was a very good Herring year.  The year-to-date Herring count was 2,386.  This is the second-best annual count after 2021. 

  • Herring numbers in LSB vary so wildly that it is hard to discern a long-term trend.
  • The March through May Herring recruitment comprises at least 90 percent of our annual numbers. The spring count of larvae and juveniles using otter trawls is crude and possibly inexact.


Northern Anchovy count = 964.  This is a very good December count.  However, the annual total of 3,962 was only average owing to the big freshwater flush early in the year.  We caught more Anchovies in 2016, 2020, 2021, and 2022.     

Anchovies generally follow the Clupeiform Color Rules but with complications.  Unlike Herring, Shad, and Sardines, Anchovies lose iridescent guanine crystals from their dorsum in low or variable salinity.


The overall number of Anchovies in 2023 was low compared to 2021 and 2022.  And, Anchovies this year appeared to be smaller and younger on average throughout the year. 

The big freshwater flush not only suppressed overall Anchovy numbers throughout the year, but it particularly seems to repel the biggest (sea-going?) adults that we occasionally see.


Baby Anchovies!  We observed larval and post-larval Anchovies at stations Coy4, LSB1, and LSB2.  Despite the population bump, the 2023 summer Anchovy spawning season was another success!  

  • Both larval Anchovies and Herring are colorless. Development of guanine appears to occur sometime after metamorphosis in both species.  


The first three Shad collected at station Alv1 were browner than the rest.  They ‘greened-up’ as we added saltier water.

American Shad count= 73.  The 2023 Shad count was 314 which is more or less average. Fifty of the Shad caught in December were from Alviso Slough alone.  American Shad, though non-native, are good-eating fish.  The scientific name, Alosa sapidissima, means “the delicious shad.”

Shad dorsal colors change very reliably with salinity.  Example: at station Alv1 on Sunday, we caught 27 Shad. 

  • We were perplexed that the first few Shad initially appeared brown. They ‘greened-up’ rapidly as we measured.
  • We quickly surmised that the holding tub had been filled with fresher upstream water before our trawl. Saltier water in the counting trays was collected on site, thus the brown shad quickly turned green!  


As expected, all Shad at upstream stations were brown  – EXCEPT ONE!

  • A green Shad was observed at station Dmp1 where salinity was well within the brown range (below 14 ppt).
  • Both brown Shad and brown Herring were documented immediately before and after this Shad was observed. There is no reasonable explanation for this green shad.
  • Perhaps, this Shad overturns the entire Clupeiform Color Hypothesis? …  Or perhaps, …
  • It’s another Fishmas miracle!!!
    (Joking aside, I cannot explain this green Shad in such fresh water. It truly is an outlier.)


The Rolling Stones – She’s A Rainbow

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