Fish in the Bay – November 2023, Cool season.

Winter fishes arrive as weather cools.  This creates a complicated picture in November. 

  • Many summertime fishes linger as Longfins, Herring, Shad, and Sturgeon show up for cool weather feeding and spawning.
  • A couple of winter flatfishes, English Sole and Speckled Sanddabs, also popped up.


Longfin Smelt numbers are increasing:  We caught 93 in October. The November catch was 114.   

Bat Rays surged.  We have never seen so many Rays this late in the year.  The additional  Rays this month put us well over the top for a new record Bat Ray year!  (We also caught some interesting oddballs this month.)  More about all that in part 3 of this report.

Musculista (Asian Date Mussel) numbers declined sharply.  Musculista are famous for rapid seasonal boom and bust cycles.  However, we suspect that something interesting might be happening here. – This will also be covered in a later part of the November report.


  • Starry Flounder numbers continue to be way above normal.
  • Staghorn Sculpin are arriving for their winter spawn.
  • Crangon shrimp bounced back surprisingly well after two bad drought years.

And, much more.


1. Longfin Smelt.

Two adult Longfin Smelt from Alviso Slough.

Longfin Smelt count = 114.  Longfin numbers increase each month as fish arrive upstream for their winter spawn.  The 2023 count is now 2419. This is just 40 shy of a new calendar year record.  The December count will almost certainly put us over the top.


Sami photographing and prepping Longfins for lab examination.  Niko records data in the background.

Sami is our master Longfin diagnostician.  He has spent countless hours in both the lab and the field assessing the health of many thousands of fish. 

  • From visual examination, Sami determined that our biggest females were at “Stage 2 reproductive readiness:” They are starting to swell with eggs, but they still need another month or two before spawning time.   


Male Longfin Smelt in Dump Slough:  With an arched and bluish back, his growing belly flap at base of the anal fin is a dead giveaway that he is a male.

 We rely on Sami to determine the sexes of Longfin Smelt at this point.  The largest fish may show some visible sexual dimorphism, but the indicators are rarely apparent in the little ones this early. 

Sex was field identified in 11 Longfins so far:

  • Alv3:  Male – 98mm and 3 Females – 96, 75, & 72mm. 
  • Alv2: Male – 96mm and Female – 92mm. 
  • Dump Slough: 2 Male Longfins – 104mm and 95mm. 
  • Pond A19: Female Longfin – 90mm. 
  • UCoy1 & 2: Male – 90mm and Female – 89mm.

All of the other hundred-odd Longfins caught in December ranged from 45 to 75mm.  Many of these smaller ones are likely reproductive as well, but not yet mature enough to show it. 

  • At spawning time, even amateurs like myself can tell the sexes on most of the fish.


2. Herring, Shad, and Anchovies.

Pacific Herring and three Anchovies at station Alv3 where salinity was high.

Northern Anchovy count = 90.  Anchovy numbers typically drop in November, so 90 is a decent count. 

Pacific Herring count = 4.  All four caught this month were young-of-year. 

  • Herring begin migrating into central and north San Francisco Bay for their winter spawn about this time of year. Relatively few of them wander this far south in the Bay, but we always find some. 


Pacific Herring and 3 Anchovies at station Dmp1 where salinity was not so high.

Clupeiform colors.  Anchovies, Herring, and Shad are part of the Clupeiform family of fishes.  You can see the family resemblance in these photos.  They all “blue up” in high salinity, and “brown down” in fresher water. 

  • Herring and Shad dorsal colors are more reliable indicators of ambient water salinity.
  • Anchovies are trickier because they slowly lose guanine crystals in low salinity.
  • The two longer and greener Anchovies in this photo do not show substantial guanine decay. We surmise that they recently arrived from the deeper Bay or ocean.   


American Shad, Anchovies, and Herring at four stations in November.

American Shad count = 7.  Shad are non-native East Coast cousins of our Northern Anchovies and Pacific Herring.  Shad do not spawn in Lower South San Francisco Bay, but we consistently catch young-of-year, year-2s, and perhaps year-3s here during their spawning season.  (Big adult Shad swim up the Sacramento and San Joaquin Rivers to spawn.)

  • Shad color is a reliable salinity indicator. (IMO: Shad never lie. They are very honest fish.) 
  • Also note: Shad blue up to a celeste (sky blue) shade of blue. Anchovies and herring blue up to a more indigo (darker blue) hue.  


3. Flat fishes.

English Sole & Speckled Sanddab count = 1 each.  Young English Sole and Sanddabs show up in LSB in winter.  These were the first arrivals. 

California Halibut count = 3.  The YTD count is 24 – a poor year for Halibut in LSB. 


Starry Flounder count = 127.  This year continues to be a blockbuster year for Starries.  Why is this year so good for them?


4. Upstream Fishes.

Staghorn Sculpins and a Starry Flounder at Alv1.

Staghorn Sculpin count = 171.  Most of these Staghorns were returning adults. 

  • This is the typical seasonal Staghorn pattern: Bigger adults start arriving in late fall.  They spawn from December to February.  Tiny babies, the size of sesame seeds, show up around February to April. 
  • Staghorns are one of several species of tough local estuarine fishes that can survive (and respire) out of water for hours or more. This survival skill is essential during the summer months when dissolved oxygen drops low in upstream sloughs.  


Prickly Sculpin count = 1.  Pricklys are fresher water catadromous cousins of Staghorn Sculpins. 

  • This fish is our sentinel species for upstream freshwater habitat: “When Pricklys are showing, the rivers are flowing.”
  • “… the coastal form [of Prickly Sculpin] lives in rivers and swims down into brackish estuaries to breed. A catadromous species, it is tolerant of high and low salinities.

Bay Pipefish count = 15.  So far, we netted 27 Pipefish in 2023.  Pipefish flourish during dry, stagnant years.  Big rains tend to disrupt their littoral lifestyle.  


Two Shimofuri Gobies and a large female Pipefish at Art1.

Shimofuri Goby count = 222.   The YTD Shimo count is 3,354.  This is a new record!  So far, Shimos continue to be our new number-one goby, by far.


5. Big Critters.

Three of four Sturgeon detections in November.

White Sturgeon count = 4.  We caught no Sturgeon in the net, but we detected four:  Two sturgeon were detected on sonar at Art3.  We saw one sturgeon jump at Coy1.  Two guys fishing had a sturgeon on hook between UCoy1 and UCoy2.

  • White Sturgeon arrive to feed in LSB marshes each winter.
  • The red tide fish-kill of August 2022 killed a large number of breeding-age adults. There is great concern that the San Francisco Bay & Delta Sturgeon population is now in peril.
  • 16 Nov 2023: Emergency White Sturgeon Regulations are now in effect     


Sami showing the male Leopard Shark caught in Dump Slough.

Leopard Shark count = 1.  The YTD count is only 9.  2023 is a poor Leopard Shark year owing to the freshness.  Frankly, we don’t know why this boy-shark was so far upstream this late in the year.


A Harbor Seal watched as we passed near station Coy4 on 11 November.

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