Fish in the Bay – February 2022: Another Record Catch.

February was another great month if you like small pelagic bait fishes. … And, who doesn’t?

  • The February Longfin Smelt count smashed all previous records.
  • Anchovy, Topsmelt, and Shad numbers continue to be at, or over, historic highs.
  • Oddball Fishes from the Sea: Several rare oddballs were caught and released:  Bonehead Sculpin, Brown Rockfish, 2 Sardines, and 2 more Tomcods.    
  • And, we caught a Sturgeon in Alviso Slough!


We may be on the brink of documenting incredible marsh recovery ~15 years after salt pond restoration in 2006...  OR, we may be seeing the effects of the cool Pacific, double La Nina, upwelling.  (More likely it is a combination of both.)  This was a phenomenal weekend for fish in any case.


Some not so good news:

  • Shimofuri Goby explosion continues: 409 Shimos/Chameleons were caught.  This month’s total was only exceeded by monthly counts in Aug, Sept, Oct, and November 2021 in the the10-year record. Non-native Shimofuri Gobies are taking over!  
  • No Herring! This is very disappointing. We saw a big surge in Herring numbers indicating a local spawning event in early 2021.  This year, Herring seem to have disappeared after January.
  • Very few Crangon shrimp. We counted perhaps 100 brooding females and less than 100 juveniles.  February is usually a low month for Crangon, but we need a big recovery.  Dry years are very hard on Crangon.   


1. Record Longfin Weekend.

Record Longfin Smelt weekend:  We caught 907 Longfins!  The previous monthly record was 456 in January 2021.  This February’s count alone exceeds the total annual Longfin counts in each of the previous 10 years!


A few of the 71 Longfins caught at station Coy1.


2. Another Record Anchovy Weekend!

Micah empties the net at LSB1: 575 Anchovies!

Near-record Anchovy weekend:  2,123 Anchovies is a February record and the 3rd highest monthly total ever.  This follows the #1 record catch of 2,934 Anchovies in January 2022.  We saw lots of babies and adults in both months.


Young adult Anchovies amongst Palaemon shrimp at LSB1 on 5 February 2022.

Anchovies: Deep thoughts about ‘Long-skinnies’ vs ‘Bay-chubbies.’  In both December and January, we caught two types of Anchovies.  The long and skinny ones were presumed to have been raised in cool ocean waters.  The shorter, full-bodied ones had the familiar shape we associate with a life-history in warm estuarine water.  We have noticed a December/January arrival of “long-skinnies” in previous years as well.

By February however, we caught no more than a few “long-skinnies.”  This could indicate that there is a very brief migration of ocean resident Anchovies into the Bay during the coldest months.  In past years, we often counted an increase in adult Anchovy numbers in December thru January and then a small drop by February. This pattern makes sense since the ocean visitors are acclimated to the coldest water temperatures. They probably tend to flee back out to sea as Bay waters warm.

  • Long-skinny Anchovy migration could represent an important wintertime conveyance of protein from nutrient-rich Bay waters out to hungry Humpback Whales, and sea birds off the coast.


Baby Anchovies!  Many of the roughly 2,000 Anchovies caught in February were larval to young-of-year juveniles roughly 40mm or smaller (babies). 


Bent Anchovies.  At least three Anchovies in February displayed this interesting form of scoliosis with two bends mid-way along the spine.  Different types of scoliosis and similar deformities in fishes have been associated with pollutants and environmental factors.  We keep an eye on this.

What causes scoliosis in fishes? 


3. Other Fishes.

American Shad:  153 were caught in Feb.  This is a high number but no longer exceptional nowadays.  For context, prior to the big freshwater flush in early 2017, the monthly American Shad count was usually zero to one or two dozen.  We catch a lot more shad now, and they are getting bigger!


Topsmelt in Pond A21 on 5 February.

Topsmelt surge continues: 84 Topsmelt were caught.  Topsmelt numbers increased after 2019.  Prior to 2020, the monthly Topsmelt record was nineteen (19).  Most of these are caught in restored Ponds A19 and A21.  Topsmelt may be a good indicator of restoration success.


Shiner Surfperch with Longfin Smelt at Art 3 on February 6th.

Only 3 Shiner Surfperch were caught in February.  Overall, Shiners have declined from common fish to rare oddballs over the past decade.  Is the local decline in Shiners a good thing, or a bad thing?


Flatfishes.  Each species of flatfish has a unique migration and recruitment pattern.  Thus far, the local abundance of each in Lower South Bay follows individual multi-year patterns:

Speckled Sanddabs show up each winter, but the catches have been highly variable: abundant in 2015-2016, rare from 2017 to 2019, then slowly increasing in 2020, 2021, and now 2022.  The February 2022 catch of 66 Sanddabs is the highest we have seen since Feb 2016.

English Sole spawn either in, or close to, the ocean.  For a few months after each December, newly hatched larvae drift or swim into the estuary to feed and grow.  Sole populations surged in 2012 and 2013 and again in early 2021.  La Nina cool ocean upwelling is known to stimulate Sole recruitment.  Accordingly, we expected Sole numbers to increase under the current La Nina conditions.  As of February, the increase has not happened.  Hopefully, we will see another surge in March.

Starry Flounder spawn far upstream at the foot of the creeks.  We had big catches of Starries in 2012 and 2017. The numbers caught since May of last year suggest they might be bouncing back again.   


As usual, our only other English Sole was heavily afflicted with internal parasites.


4. White Sturgeon

Left panel:  Micah dons makeshift hand protection.  Right panel: Micah and Alec heft the big fish onto a soft net bedding for measure and release.

White Sturgeon.  We netted this Sturgeon at station Alv2.  It was 1.5 meters long (just over 5 feet).  At that length, this fish is still young by river monster standards; about 18 to 20 years old according to the charts.  This one is getting close to the upper slot limit for a legal catch.  If this teenage Sturgeon can resist the urge to take an angler’s bait for another few years, he, or she, might be visiting this slough well into the 2100s!


Micah releases the sturgeon back into Alviso Slough as Western Sea Kayakers club members cheer.


5. Oddballs from the Sea.


It was a good month for coastal oddball fishes in Lower South Bay.  The estuarine thermal barrier was down: local water temperatures dropped close to single digits.  At least four unusual visitors were observed.

Brown Rockfish (aka Chocolate Bass or Brown Bomber).  Brown Rockfish are commonly caught just north of Dumbarton Bridge.  But, this is only the second one we have caught this far south.  They hide in sea grasses and rock crevasses in coastal areas from Baja to Alaska with a lifespan up to 34 years. 

Bonehead Sculpin.  We catch one of these odd sculpins every year or so.  In fact, the last one was caught this time last year.  There are many similar-looking, and probably closely-related, sculpins that inhabit California’s coastal waters and tide pools. For that reason, I can’t find much information about this particular variety. … Judging from the shrimp’s antennae sticking out of its mouth, we can confirm that Boneheads eat shrimp.   


Brown Rockfish, Bonehead Sculpin, and Chameleon and Shimofuri Gobies in the Photarium, LSB1 on February 5th.


Brown Rockfish (top center) and Bonehead Sculpin (bottom center), LSB1, 5 Feb 2022.


Pacific Tomcod (top) with three Speckled Sanddabs, Coy3, 5 Feb 2022.

Pacific Tomcod.  We caught Tomcods in December, January, and now this one in February.  This is a Cod relative that lives on the coast.  Tomcods rarely swim this far into San Francisco Bay.  This specimen has a very full, pregnant-looking belly.


Same Tomcod showing off the full, pregnant-looking belly.

Tomcods only grow up to a foot long.  She measured 148 mm (just shy of 6 inches).  Could such a young and small Tomcod be full of eggs?  If not, then she is certainly eating well. 


Pacific Sardine.  The Sardine is the common sea-going Clupeiform fish that we practically never see in Lower South Bay.  We have only seen one Sardine in the past.  Now, we have two.  How and why did they arrive?

Two young Sardines probably don’t signify much.  But, on the grander scale, there is a fascinating collection of articles and published studies that investigate the puzzling relationship between proposed ‘Sardine versus Anchovy Regimes’ in the Pacific and Atlantic oceans.

As I understand it, the general Sardine versus Anchovy rules are:

  • Sardines are specialized to feed on tiny food a little farther out in ocean waters.
  • Anchovies are adapted for life closer to the coast and eat a wider range of small critters from fine to coarse.
  • Anchovies generally flourish when the overall ocean cycle is in a cool phase and upwelling is strong near the coast.
  • Sardine populations surge with under a warm ocean phase with high primary productivity at sea and/or when Anchovies become scarce.

Sardine vs. Anchovy rules were derived from many years of highly variable catch data and inexact sediment proxy records.  They are very much subject to revision with each new published paper:


6. Red Tide at Station Alv3?

Red Tide?  Water color was strange in Alviso Slough on Saturday, February 5th.  It was very brown when we launched at Alv1.  This was not too unusual.  Water flowing from Guadalupe River is often very brown here. But, Dissolved Oxygen (DO) readings were very high at each station.  DO reached 125 percent at Alv1, 130 percent at Alv2, and then climbed to 169 percent (16.4 mg/l) at Alv3.

Micah first noticed a reddish tinge in the water as we approached station Alv3.  The weather was sunny, bright, and cool.  The water surface was like glass, and salinity readings indicated a fair amount of stratification below. 

The reddish tinge was concentrated near the surface.  Streaks of redness swirled when we probed with a Secchi disk, and browner water upwelled from beneath.  It suddenly occurred to all three of us that this could be a Red Tide!


Red tide in a bottle.  A red tide could be both very exciting and very troubling:  Exciting because dinoflagellates (“Dinos” – the unarmored types) are the most nutritious food for baby Anchovies and other tiny fishes.  But, the types of ‘Dinos’ that cause red tides can also be very toxic.  What are we seeing here?

If this was a red tide, it was not very intense.  We saw no ugly surface scum at Alv3, smelled no foul odors, and observed no stress or sickness in the fish and bugs.  Just to be sure, we collected a water sample in an empty bottle and packed it in ice in case anyone at the OG Fish Lab might want to analyze it. 


7. The Garbage Patch.

Prevailing winds blow towards the southeast across Pond A19. For years we observed a growing Garbage Patch accumulate in the Pond’s southeast corner.  The patch encompassed a depressing collection of plastic bottles, buckets, soccer balls, and random litter.  We picked up and photographed a few loose pieces whenever reachable from the boat. But overall, the Garbage Patch slowly grew.

Then, something miraculous happened:  The Garbage Patch was gone when we visited in February.  For weeks I wondered, where did all that trash go?  Eventually, I learned from ‘Salty Dave’s blog’ ( that Eric Larkin and the Western Sea Kayakers club were responsible for this cleanup:

“… on January 18th, club members Steve Ochoa and I joined Ducks Unlimited biologist Kate Freeman as volunteers to scout out Alviso Pond A19 at the Don Edwards San Francisco Bay National Wildlife Refuge as a potential site for trash pick-up days and to pull out what trash we could ourselves.”

What an improvement!  This corner of Pond A19 is a productive spawning place for Longfin Smelt, Anchovies, Staghorn Sculpin, and probably Topsmelt as well. With the garbage gone, it truly looks like a restoration success!

Thank you Western Sea Kayakers, Ducks Unlimited, & Salty Dave for cleaning up this mess!

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