Fish in the Bay – October 2021: Longfins Returned. Non-native Silversides & Shimofuris were still out of control.

Trawl map.

The results from October trawls were a mix of good and bad news on several levels.


Bay-side stations trawling results.

Bad News.

  • Only 48 Crangon shrimp were caught in October. This is not the worst October we have ever seen, it’s just the worst since 2016.  And at the same time, the non-native Palaemon Shrimp population surged to the highest numbers seen in several years of trawling. 
  • Non-native population explosions of Inland Silversides and Shimofuris continued. The only mitigating factor is that both species seem to be fairly contained at upstream fresher water stations.


Upstream of Railroad Bridge.

Good News.

  • Longfin Smelt returned for spawning!
  • The Anchovy spawn continues. But, the spawn was somewhat interrupted by the arrival of a new cohort of colorful adults.
  • Other good news: Bat Rays and Leopard sharks kept showing up at far upstream stations.  This is probably due to persistent high salinity.  Also, adult Staghorn Sculpin began returning home for spawning.  All these fish help control non-native pests and are always a welcome sign.


Great Egret on patrol at Alv1.


1. Shimofuri and Silverside Population Explosions

Tray full of 863 Inland Silversides and 857 Shimofuri Gobies at Alv1 on 17 Oct 2021.

Shimofuri Gobies.  The Shimo explosion began in August when 688 were caught – most at Alv1. Then, we counted 816 in July, then 997 this month.

Inland Silversides.  The current Silverside count is only dwarfed by that of the previous year. Silversides exploded in July, September, and October of 2020.  Last year’s November cold snap knocked them down, but they came back again this summer.  The annual Silverside bloom coincides with our Anchovy spawn, and that may not be accidental.


Huge population explosions of non-native Inland Silversides & Shimofuri Gobies continued to increase at upstream stations through October.

Shimos (orange in the above graph) arrived in SF Bay sometime in the 1980s.  They were first positively identified in LSB in 2014 when three (3) were counted.  The annual Shimo count increased to tens then hundreds over the subsequent six years.  Now, the 2021 count stands at 2763 with two months still remaining! 

Silverside numbers have also increased in recent years.  Fortunately, they die back after the first winter chill which could protect Longfin Smelt eggs and young from being eaten.


2. Topsmelt

Topsmelt and Silversides:  Five Topsmelt are shown at center.  Two Inland Silversides are at top and three or for more near bottom.  Alv2, 17 October.

Topsmelt. 118 Topsmelt were caught in October.  This is our second highest catch in several years of trawling. 

Native Topsmelt are members of the “Atherinidae,” aka “Silverside,” family of fishes along with Jacksmelt and Grunion.  Inland Silversides are also members of this family.  In photos, you can see a mirror-like band along their sides that give them the family name.


Yellow splotches.  In October, most Topsmelt we caught were larger than usual and had yellow splotches on the sides.  Years ago, Dr. Jim Hobbs told me that yellow splotches on Topsmelt indicated sexual maturity. 


3. Longfin Smelt.

Two young-of-year Longfin Smelt at Art1.

Longfin Smelt.  37 Longfin Smelt of the season were collected in October.  These were the first arrivals for the 2021/22 spawning season.  All but five Longfins were caught at upstream stations in October. They seek cool brackish water for spawning.  


Larger male Longfin.  A Cymothoid Isopod had just crawled out of the gill. UCoy1.

Unlike Topsmelt, Longfins are true smelt of the family Osmeridae.  This makes them cousins of the endangered Delta Smelt in California, the Eulachon in Washington State, and many other species in Northern Europe and East Asia. 


4. Cymothoid parasite as surrogate indicators of Shad & Longfins.

Cymothoid Isopods = Devil Bugs!  We caught 9 of these bugs in total. They always show up in late fall to early winter as water cools and Shad and Smelt start running upstream.  These marine hitchhikers are forced to abandon their host when the fish swims into fresher water.  They seem to be reliable surrogates that indicate Shad and Longfin arrival, so we added them to the list of critters we regularly count.

  • At least four were too large to fit into Longfin Smelt gills.  We presume the larger bugs detached from American Shad.  
  • Cymothoids are very interesting bugs.


5. Starry Flounder & Sculpin.

Three Starry Flounder & a Staghorn Sculpin at Art3 on 16 October.

Starry Flounder continued to migrate up the main stem of Coyote Creek for their annual spawn farther upstream.  We counted 17 Starries in October,  The 2021 count stands at 55 so far.  We have seen worse years, but in good years we have seen a few hundred by now.  

Staghorn Sculpin.  Staghorn numbers jumped to 54 this month as they started to return for their winter spawn here in the salt marsh.  2021 continues to be our second-best Staghorn year after 2012. If La Nina ocean upwelling is the key to Staghorn recruitment, then 2022 may be our best Staghorn year yet! 


6. Bay Pipefish

Bay Pipefish.  Eleven Pipefish were caught and released in October.  So far, 2021 has been just an average year.  We catch them at all stages of their life cycle, from tiny babies to pregnant adults. 


7. Anchovies!

Northern Anchovy.  We caught 456 Anchovies in October.  That is a good monthly catch, and 2021 has been a good Anchovy year. 

But, something changed in Anchovy world.  Many of the October Anchovies showed more color than they did in September.  They were also less inclined to express eggs or milt during random egg checks.  Reproductive readiness seemed to have fallen off.  


More large and colorful Anchovies in Dump Slough on 16 Oct.

We presume that a new cohort of Anchovies, fresh from the ocean, may have arrived.  Crisp blue and green dorsal colors tell us that these fish are not yet acclimated to low salinities in Artesian, Dump, and Upper Coyote Sloughs. 

Or perhaps, these fish spawned out earlier in the summer, migrated to the Bay, and then returned again?  What is going on here?


Golden Anchovies at UCoy1.

As usual, ‘browned-down’ golden Anchovies were still found at fresher upstream stations.  … Newly hatched Anchovies flee downstream soon after metamorphosis. 


8. Sharks & Rays.

Brown Smoothhounds.  Six Brown Smoothhounds were caught in October: three at Coy3 and three more at Coy4.  This was very unusual.  We have never seen more than four Smoothhounds in any previous year.


Parasite Damage.  Either the fresher water of Lower South Bay doesn’t agree with these young Smoothhounds, or the parasites don’t.  They were heavily infested. The damage caused by blood-sucking copepods was grotesque.



Too many parasites!!!

At both stations, each Brown Smoothhound, aka dogfish, hosted several to dozens of copepod parasites.   Each parasite was carefully removed for close examination.  We counted over 60 of them; at least 10 per shark!


One of five Leopard Sharks at Coy1

Leopard Shark pups grow larger every month through the warm season.  They are susceptible to the same parasites as Brown Smoothhounds. But for some reason, they host far fewer copepod bloodsuckers.  Leopard Sharks may be better adapted for life in brackish estuarine waters. 


Seven baby Bat Rays at UCoy2 on 16 October.

Bat Rays.  2021 has been an exceptional year for Bat Rays.  With the 32 caught this month, the year-to-date count is 118.  This is our best year on record. 


The vast majority of Bat Rays caught in 2021 have been babies.


9. Shrimp Wars.

Younger, clear-bodied Palaemon & one Oregon Mud Crab at Coy4

Palaemon Shrimp continued to dominate shrimp world.  Over 10,000 Palaemon were caught in October alone!  That’s as many as we have seen in most good years.  The 2021 Palaemon total has already broken the ten-year record.  

Literature says that larger and older females migrate upstream to release broods during the warm season in their North-East Asia homeland.  Males and younger shrimp tend to loiter downstream.  Though we don’t carefully document the Palaemon life cycle here, photos and general observations seem to confirm that pattern. 


Three Crangon shrimp amidst Palaemon at UCoy1 on 16 October.

Crangon Shrimp.  Only 48 native Crangon were seen in October.  Crangon numbers were high for the first part of 2021.  Then for some unknown reason, the population abruptly crashed even as Palaemon numbers continued to increase after June.

Historical sources tell us that Crangon were much more numerous here before over-fishing, pollution, and habitat destruction took their toll.  All of those ills have been gradually alleviated.  Nonetheless, a back-and-forth competition between Crangon and non-native Palaemon started in the 1950s and persists to this day.  


10. Some Bottom Dwellers.

Corbula Clams.  The 2021 Corbula count is now roughly 3,500.  The total was a bit higher the last few years, but much lower in 2013 through 2015.  The first full year of otter trawls in 2012 was by far the record-breaker when tens of thousands of clams were counted.

It’s hard to say what combination of factors keep these ecosystem-destroyers under control in Lower South Bay, but it definitely is a combination.  

  • Wet versus dry years do not explain the rise and fall of Corbula Clams.
  • Diving ducks and baby Bat Rays consume them upstream.
  • Tunicates, barnacles, anemones, and other sessile marine organisms anchor themselves to hard Corbula shells downstream.
  • Philine snails and Atlantic Oyster Drills probably eat Corbula as well.


Red Ceramium Algae practically disappeared by October!  This one-to-two-foot tall forest of red algae spread across most of Lower South Bay in July through September.  It clogged our net on every trawl at stations LSB1, LSB2, Alv3, and Coy1 through Coy4 in mid-summer.  And then, it went away.  Only a few fragments were found at downstream locations. 

This same pattern occurred in 2020: a massive summer Ceramium bloom was followed by a complete die-back.  This alga must impose a profound change on the bottom ecology when it blooms.  What causes it to die back?  Where do dead rotten algae go they die?


Enosima Aeloid (Sakuraeolis enosimensis).  Another specimen of our new nudibranch was picked up at Coy3.

  • A video of beautiful nudibranchs: (I believe the similar-looking one with the red mustache in this video is the San Francisco Bay native Hilton’s Aeolid (Phidiana hiltoni)):  


11.  Life goes on.  

American Avocets loafing in Pond A19 on October 16th.


Harbor Seals lounging at Calaveras Point.  After summer molting season, most red seals show their true colors.


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