Fish in the Bay – May 2023, Extra Baby Fish Month.

More baby fish showed up in May.  For want of a better term, this was an “Extra Baby Fish Month.” This extra baby fish month was a little later than most we have seen before.  And, by several measures, May was a strange month; different from any we have seen before. 

  • Yellowfin Goby numbers are still low. Something suppressed their spawn a bit this spring. 
  • Baby Starry Flounder explosion: 345 Starry babies.  That is the biggest Starry recruitment we have ever seen
  • Baby Herring persist. Another 300 were caught in May.  Herring are usually gone after April.
  • Baby Longfin Smelt explosion. We have never seen so many Longfin babies.  We rarely see Longfins at all after March or April.   

Abundant rains from numerous Atmospheric Rivers greatly helped Flounder, Herring, and Longfins.  However, the possible causes for low goby counts remain unknown.

Bonus article.  Clara Mokri, a photographer from SF Chronicle, joined our trawls in May.  With inspiration from the photographic evidence, Tara Duggan wrote this article:  “S.F. Bay is no longer an environmental disaster. Here’s what drove incredible transformation.” 


Some of the 653 larval Longfin Smelt and other baby fishes collected in Pond A21 on 7 May 2023.

Smeltnado.  Good News!!!  May is our new record Longfin Smelt month!  1,184 Longfins were caught.  This beats the previous record of 895 in February 2022.

  • Between 2014 to 2016, Dr. Hobbs found NO EVIDENCE of Longfin Smelt spawn in these LSB trawls.
  • Smelt are recruiting now! Spawning Longfins may have achieved critical mass in the Alviso/Coyote Creek marshes!      


Many baby fishes at upstream stations.


Many more baby fishes and Crangon at downstream stations.


Sami and Micah demonstrate the delightful benefits of wearing Grundens foul weather gear.


1. An Extra Baby Fish Month.

Sami and Micah counting baby fishes.


Baby fishes appear as a gelatinous mass when sieved through the net.

This group from Pond A19 included many baby Longfin Smelt, some baby Yellowfin Gobies, and at least a few baby Herring.  Bugs like Crangon, Palaemon, and Mysid shrimp were mixed in as well.


The late-season appearance of Longfin Smelt babies was unexpected.  Many baby fishes were preserved and taken back to UC Davis CABA lab to be certain of the identification.  Lab analysis confirmed that this was an extraordinary recruitment of baby Longfins!


Some random representative examples of baby fishes seen in May.


The Longfin Smelt spawn of 2022/23 was the biggest we have ever seen!


 More than half of all baby Longfin Smelt were caught in Pond A21!

As a rule, babies are counted quickly and released like all the other fishes.  However, his May event was unexpected and unique.  This one had to be carefully documented. 


2. Goby World.

Gobies.  Overall Goby counts remain a little low, particularly for Yellowfin Gobies. 

  • So far, unidentified/baby goby counts were 929 and 484 for April and May respectively.
  • Yellowfin Goby counts were just 28 and 83 for the same months.
  • We usually see several hundred to a few thousand Yellowfins by this time of year.


There is much variability in goby numbers from one month to the next. Typically high goby counts we see in April established a tradition of “Baby Fish Month.”  However, the reality is a ‘baby fish season’ that extends from around March to as late as July.  It just usually appears to peak around April when most of the Yellowfin Gobies hatch.

For 2023, Yellowfin Gobies have not surged.  We saw a similar lack of Yellowfin recruitment in 2019 which was also a relatively wet year.   But, the spring of 2017 was also very wet, and yet, Yellowfin recruitment was robust, albeit did not peak until July.

If there is a general rule, it may be that Yellowfin populations tend to increase in dry years.  Rainwater flushing seems to knock them back a bit.  More investigation is needed!


3. Herring, Sculpin, & Sole.

Herring, Sculpin, and Sole are other baby fishes that show up in springtime.  Populations of all three are stimulated by La Nina upwelling off the coast. But, their spawning and recruitment in SF Bay is also heavily dependent on robust winter rains.

  • Counts of all three species peaked in 2012 (following the 2010-11 La Nina?) and again in 2021 – and to a lesser extent in 2023 (This was during the extended 2020-22 triple La Nina.)
  • Numbers were low following the 2014-2015 El Nino.
  • Is this random noise? (I have long hoped to establish some kind of “La Nina” connection with them using LSB data alone. As always, the data is messy.)  Conclusion:  Insufficient data.  There could be a La Nina connection here.  Or maybe not!        


Staghorn Sculpin count in May: 517.  Some Staghorns were still showing up as babies.  Most youngsters have grown bigger.


A young Herring amongst many young Staghorn Sculpin. 300 Baby Herring were counted in May!


4. Starry Flounder.

Starry Flounder.  We counted 345 Starry babies in May.  This was a big surprise.  Normally, we see only one to a dozen Starries in any given month.  …  345!!!

  • Big rains may have helped increase Starry numbers this spring. However, we did not see so many Starries in the other big rain years of 2017 and 2019.
  • Eleven years ago, in June 2012, we caught 326 young Starries. That was the only other Starry recruitment we have ever seen that comes close to this one. 
  • What makes Starry recruitment boom and bust like this?


Restored Pond A19, 6 May 2023.

This place is getting greener.  The restored ponds have become gardens compared to what they looked like as late as 2014 and 2015. 


5. Deep Bay Fishes.

Sami & Micah calm a large male Bat Ray (450 mm wingspan!) prior to measurement & release at LSB1.

Bat Rays.  Three Rays were caught in May.  Last year, 2022, was our record year for both Bat Rays and Leopard Sharks.  Due to the current water freshness, we will not see so many sharks and rays this year.


Young and older Anchovies at LSB2 on 7 May 2023.  Photo by Janai

Anchovy count: 1,335.  This is a May record.  But, this month’s surge is a little different than previous years.   Usually, the late spring Anchovy surge is comprised entirely of adults.  This batch is a mix of adults with many that are clearly very young.

  • Was there a late 2022 second wave of spawning last year?
  • Or, did many of these young Anchovies hatch elsewhere in the Bay or out to sea?


6. Bugs.

Crangon Shrimp count: 7,444.  For this time of year, this is just average. 

  • In good years, like 2018 or 2020, Crangon numbers peaked around July or August.
  • In not-so-good years, the numbers crashed and fizzled after June.
  • If we see high numbers from now until August, it could be a fairly good Crangon year.


Mollusk Collage.  Photos by Janai.


Isopods.  Photos by Janai.

Isopods in LSB are non-native and long-established.  They are detritivores and not particularly harmful, as near as we can tell. 

Sow Bugs – Synidotea laticauda crawl on the bottom in brackish to marine water:

Pill Bugs – Sphaeroma quoianum is one of at least two varieties of Sphaeroma pill bugs we see here.  They burrow into mudbanks in fresher brackish water.  We rarely see them at saltier downstream stations.


Janai shows off a Harris Mud Crab at UCoy2.  This one is a female full of eggs.


Pile Worm (Nereid Polychaete) at UCoy2.  Photo by Janai.


7. Plankton World.

Janai examines a water sample using a field microscope on May 6th.

Janai Southworth joined our May and June trawls to examine phytos and zooplankton that feed our baby fishes.  She has performed plankton sampling and microscopic analysis for NOAA around the Farallon Islands and as a hobby in north San Francisco Bay for many years. 

Janai is helping us explore the microscopic life that feeds our baby fish nursery.  These are a few initial observations.


The first thing Janai noticed in Lower South Bay was a great abundance of pennate diatoms.  Centric diatoms and dinoflagellates were relatively scarce compared to what she normally sees in central San Francisco Bay closer to the cities of Oakland, Alameda, and San Francisco.

According to Janai, this makes some sense because pennate diatoms tend to prefer shallower and warmer waters.  


Centric Diatoms, like Thalassiosira and Coscinodiscus (shown here) were present, but not nearly as abundant – at least in May.


Many, many Tintinnid ciliates were observed at upstream stations in May.  Tintinnids have hard vase-shaped shells called “lorica.”  (The name “Tintinnid” is derived from a Latin word for a small bell.)


Copepods, and particularly very young Copepod nauplii, like this one, are very good food for small fishes.  Copepod numbers seemed to be higher at downstream stations in both May and June. (Notice the bright red eye in this specimen.)


These were just a few early highlights from Janai’s microscope.  The hard work of evaluating and tracking this micro world has only begun.


“Time is the measure before it’s begun
Slips away like running water …”

Yes – Does it really happen?

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