Fish in the Bay – April 2024, Part 2, Every Fish has a Season.

This is part two of the April report.  Part one covered “Baby Fish Month” which mainly pertains to the April Yellowfin Goby hatch. 

However, there are over 35 species of fishes in Lower South San Francisco Bay (LSB).  Fish spawning cycles extend throughout the year.  We can learn to read each cycle like the backs of our hands – metaphorically speaking.  

1. End of Winter Fish Season.

Longfin Smelt count = 1.  This was the last adult Longfin of the season.  (Longfins had already abruptly left the upstream spawning grounds for deeper water in March.)

  • We have had Aprils with NO Longfins … but not since 2018, 2016, and earlier.  This might be the first of several El Nino disappointments. 


American Shad count = 1.  April is also typically a low Shad month.  Like the Longfins, Shad seek cooler waters in summer. 

  • Good news: This single Shad of the month was a little bigger and chubbier than we typically see here. Maybe big Shad will one day choose LSB creeks as a new spawning place.  Who knows? 


2. Striped Bass.

Striped Bass count = 15.  All but three Striped Bass were small young-of-year ~ 100 to 150 mm.  The three exceptions were still smallish ~ 265 to 285 mm. 


3. Fishes pushed downstream by low salinity.

Pregnant mama Shiner Surfperch at Alv3, 7 Apr 2024.

Shiner Surfperch count = 2.  Both Shiners caught in April were pregnant.  (Shiners give live birth.  Females are literally “pregnant,” not “gravid” with unfertilized eggs like most fishes we see.)  Shiner females search for brackish marsh to deliver up to 40 thumbnail-sized young.


Bay Pipefish count = 9.  Pipefish were growing bigger and getting ready for their spawn.  Some males were showing swelling belly pouches.  Females show a hard upper belly as eggs develop. 

  • Adult Pipefish were also showing up miles downstream from their usual hangouts. 


Northern Anchovy count = 595.  This is the second highest Anchovy count we have seen in an April.  (714 Anchovies in April 2015 was the record.)  April is typically a “low Anchovy” month before summertime spawners start migrating in.     But ….

Something’s wrong with this picture.  We spotted this school on sonar at LSB2 just before bringing it in the net. 580 Anchovies were caught here versus only 15 Anchovies the rest of the weekend.

  • We were just lucky to intercept this school.


Another thing wrong with this picture:  Few, if any, of these fish were old enough for spawning.  Roughly half were juveniles no more than a few months old.  

These youngsters have not yet been exposed to sufficient salinity to develop dorsal color.   Their dorsums appear almost transparent.  (This brownish color is NOT an indication of low salinity, but rather the color of fish muscle and viscera under a layer of translucent flesh.)

  • Anchovies require exposure to higher salinity to develop iridescent planar guanine crystals.
    • How much salinity? How much exposure?  (We still don’t know!)  Investigation continues.
    • Salinity at LSB2 was 17 ppt in April and 16.6 ppt in March.

Adult Anchovies should be starting to stage for the summer spawn.  Where are they?


4. Freshwater Oddballs venture into our trawling range when salinity is low.

Sacramento Sucker at Art2

Sacramento Sucker count = 1.  Suckers are common in freshwater creeks, but we only see them in our downstream trawling area in the wettest years. 



Common Carp count = 3.  Big rains and extended rainy seasons allow Carp to wander downstream at their peril. 

Salt marsh is harsh on Carp.  Carp are stressed by brackish salinity.  Some combination of osmotic stress and saltwater predators seems to eat Carp alive!  Their tail fins are often deteriorated or bitten off, and other grievous wounds appear.  

  • Top Panel: Consistently fresh healing waters of Artesian Slough sustained this beautiful Carp.
  • Bottom Panel: Coyote Creek water at UCoy2 is very fresh but variable. This Carp looks bitten on the tail fin, at the base of the anal fin, and under the jaw.
  • Right Panel: Dump Slough is also very fresh but variable. This fish had been attacked by something very big and strong. We first suspected Lamprey damage. But, this location is also roughly a mile away from the Bald Eagle nest in Milpitas where two baby Eaglets hatched this spring.  Could this be Eagle damage?!?!?   



Prickly Sculpin count = 6.  Pricklys migrate downstream from freshwater creeks to spawn when rainwater flow is high.  This one adult was caught in April.  Five others were tiny babies.



5. Staghorn: the other Sculpin.

Staghorn Sculpin count = 41.  This count was disappointing.  In April, we usually see a hundred to as many as a few thousand young fingerling-sized Staghorns, plus a few spent adults. 

  • Literature identifies Staghorn Sculpin as a “La Nina fish.” Our LSB data confirms that bigger baby booms happen during La Ninas.
  • Our worst April counts to date were during El Nino years of 2015-16.  



6. Flatfishes.

English Sole count = 4.  Another disappointing catch.  Fry hatch off the coast and drift into the Bay to recruit.  In good years we count hundreds to thousands of Sole in spring. 

  • English Sole is another La Nina fish. Most of our best Sole catches were during the recent triple-dip La Nina. 
  • El Nino is bad for Sole.    


Three Halibut (top left), two Starry Flounder (far right), and one English Sole (bottom center) at Alv3.

California Halibut count = 14.  The Halibut count was decent, but still a bit low for an El Nino year. 


Starry Flounder count = 32.  This Starry count was yet another record at the end of 12 months of record catches:  In May 2023, we caught 345 baby Starries.  Dozens to hundreds of young and growing Starries showed up each subsequent month.  The Starries had grown to robust-looking young adults as of April.

  • Confirmation of continued Starry success depends on another record hatch this May.
  • Bad News: We already trawled in May (report to follow). We found no babies and only 4 older Starries.
  • Now we can only hope that baby Starries may still show up in June.



7. Gobies with Chubby Cheeks.

Shimofuri Goby count = 57.  Summer is Shimo spawning season, and this puffy-cheeked Shimo is a harbinger of the spawn. …

New Discovery! (for us anyway.)  We came across this Shimofuri with grotesquely swollen cheeks in Pond A21.  We had seen this before on a few occasions in past years.  Until now, we assumed that puffy faces in gobies was a result of buccal respiration.  (, this Shimo’s cheeks did not deflate when he was put back in water.  In fact, his cheeks appeared to be unable to deflate at all.  What is going on here?

A similar characteristic is described in “Round Gobies” from the Caspian region. 

I contacted Mr. Munenori Kishida, lead scientist for Emperor Emeritus Akahito at the Biological Laboratory of the Imperial Palace (BLIP) in Japan.  He and his group are the world’s experts on Shimofuri and Chameleon Gobies.   Mr. Kishida confirmed that swollen cheeks are often seen in both Shimofuri and Chameleon Gobies as well as other members of the tridentiger (Triple-toothed) genus of gobies.   

Mr. Kishida provided several points of additional information:

  • Individuals with swollen cheeks are always adult males, but adult males with ordinary cheeks are also often observed: Swollen cheeks are sometimes seen in male gobies smaller than 50 mm (SL), and some males gobies larger than 50 mm do not express swollen cheeks. This implies multiple reproductive strategies or tactics amongst males.
  • Adductor mandibulae muscles, the largest head muscles in gobids, are responsible for this swollen characteristic.  However, the trigger and mechanism for developing swollen cheeks remains unclear.
  • These muscles are thought to be important for reproduction by facilitating nest construction, nest guarding, and for removing mold and debris from eggs.


Yellowfin Goby count = 62.  Non-native Yellowfins have been our number one goby for decades after their introduction into San Francisco Bay in the 1950s.  But, Shimofuris have been rapidly over taking them in LSB. 

The Yellowfin Spawn has just ended.  These three rather skinny-looking males have probably just emerged from three to four weeks of fasting while each guarded a burrow full of eggs.

  • The male at top is showing the characteristic “broadened head” – equivalent to swollen cheeks in Shimofuris.
  • Mr. Kishida at BLIP also mentioned that cheek swelling and/or head broadening is likely a common mating season characteristic amongst males of many species of gobies.  


Cheekspot Goby count = 6.  Tiny native Cheekspots also spawn in the warm season.  The swollen-head characteristic is harder to see due to their miniscule size, but macro photography helps reveal it.

  • Blue-black cheek-spots enhance this male’s mating display.
  • This may explain why the spot is an unreliable identification feature for Cheekspots: The spot may be absent or muted in females.  It may be muted in “sneaker males” as well.  (Assuming Cheekspots have sneaker males.)   

Swollen/chubby cheeks tell us when goby spawning season has begun!

Comments are closed.