Fish in the Bay – May & June 2020, part 2: Fishes of June, plus a bonus worm.

This is part two of a combined May – June report.  Part one examined the massive Crangon shrimp recruitment explosion that peaked in May along with some odd marine invertebrates. 

This report focuses on the fishes, particularly those caught and photographed in June.


Trawl map.


Bay-side stations trawling results.


Upstream of Railroad Bridge.

June data tables are shown above.  Our drier weather, summertime fish have returned:  California Halibut, California Tonguefish, Staghorn Sculpin & Northern Anchovy.  All four species tend to do well in Lower South San Francisco Bay when it gets warmer and saltier. 

Good News: The total fish count was 1158, which is a decent haul for a June. Other highlights:

  • An unusual burst of 53 Top Smelt occurred in Pond A21.
  • Rare catch of three Longfin Smelt in a warm summer month.
  • Plus, we saw a fairly substantial rebound in Yellowfin Gobies. I was hoping these noxious, non-native invaders were on their way out for good.  But alas, hundreds of baby Yellowfins showed up in both May and June.  


1. Weird Fishes.

California Halibut from station LSB1.

California Halibut.  Three of the six Halibut caught at LSB1 on Saturday are shown above.  As mentioned before, California Halibut can be either “right-eyed” or “left-eyed.” 

Young Halibut tend to show more splotches and spots.  The brown color gets more even as the fish ages.  Halibut also change color to match their substrate.  Based on that, we could guess that two of the three above were netted from a sandy or shell-hash bottom.  Halibut #3 may have been laying on a muddy bottom?    


California Tonguefish and one Plainfin Midshipman from Station LSB2.

California Tonguefish.  We caught five of these weird fish at LSB stations in the deep Lower South Bay.  They are roughly the size of a tongue, have a tongue-shaped body, two tiny eyes, and a hook-shaped mouth – and that’s it!  These are native to the area, but have no commercial or recreational value to humans, ergo, not much is known about them.  Supposedly, they eat tiny amphipods.  Leopard Sharks, Bat Rays, and other large bottom-feeding predators probably eat Tonguefish.    


Plainfin Midshipmen are bioluminescent, and they sing up to several songs!

Plainfin Midshipman.  Every summer, around this time, we catch a few to several of these strange fish at Coy4 or deep LSB stations.  These are the “California Singing Toadfish” that were famous for keeping houseboat people awake in Sausalito back in the 1980s.  The two shown here are babies. 

Large male Midshipmen (Male Type 1) sing in a low pitch hum to attract a mate to their rocky lair near the water’s edge.  They can hum continuously for up to 2 hours!  They say this is the longest vocalization by any animal on the planet!  I mention “male Type 1” because Midshipmen come in three sexes: large Male (Type 1), smaller Male (Type 2), and Female. 

These fish are also bioluminescent; their rows of photophores resemble the buttons on a midshipman’s coat, hence their name.  They “light up” to attract prey at night.  (Some photophores are visible as rows of tiny dots over the heads and parallel to the dorsal fins in this photo.)  

As fish go, Midshipmen are more magical than weird.  


Longjaw Mudsucker from Pond A21.  This fish can breathe air for hours when stranded out of water.

Longjaw Mudsucker.  17 Mudsuckers were caught in June.  Males fight for prime burrow sites along muddy fringes of pickleweed marsh.  Most that we catch by net in Pond borrow ditches or the main slough channels are smaller younger fish that have not yet settled into a good defensible burrow.    

Alpha male Mudsuckers grow ridiculously long upper jaws (maxillae) that extend back alongside the head like a pair of horns.  I gather they use their giant mouth for battle against other males and to eat small fish and invertebrates.

As mentioned many times, this fish has the amazing ability to gulp air for hours if stranded when the tide goes out.  


Bay Pipefish and baby Starry Flounder from station Dmp2.

Starry Flounder & Bay Pipefish.  These two fish are common here.  Nonetheless, they are also weird.  The pipefish is an adult.  The tiny Starry Flounder shown here is very young – less than 2 inches long and probably only weeks old.


Two Pipefish were caught during trawls in June.

Bay Pipefish males, like their seahorse cousins, store fertilized eggs and young in a belly pouch.  The Pipefish collected and released at station Alv1 appears to be a “pregnant” male.  By end of June, he should have released his new brood.


2. Baby Fishes.

Top Smelt.  We netted a cluster of 53 baby Top Smelt in Pond A21.  It is unusual to catch so many in the otter trawl. (The fish is common, but the otter trawl net does not easily catch it.)  There must have been a substantial spawn event in the pond recently.  Adult Top Smelt grow to over 14 inches.


Jacksmelt eggs on seaweed.

Jacksmelt eggs.  Our June Top Smelt catch reminded me that Luisa Valiela emailed another photo of Jack Smelt eggs she found attached to red and green algae in late April.  For the second year in a row, Luisa found her dog eating seaweed along the shore near Emeryville.  The seaweed was covered in tiny Smelt eggs.  Both smelt eggs and red algae are traditional delicacies amongst many human cultures – dogs eat them too!   

Our estuarine fishes spawn at predictable times of the year based on temperature and salinity triggers.  The spawning sequence in Bay marshes follows roughly this timeline: **

  • Longfin Smelt – January and February. (The official Longfin spawning story is “November thru May, peaking in February through April.  However, the outer dates may apply more to the inland Delta where winter temperatures drop into the teens over a longer period.
  • Pacific Herring – no later than March.
  • Jacksmelt and Top Smelt – later spring, after March.
  • Northern Anchovy apparently spawn somewhere in and around the Bay in late fall.

** Comments and suggestions are welcome.

The timing and successes of each spawn are good indicators of ecological health of our marshes!


Three Longfin Smelt caught in June trawls.

Longfin Smelt.  Three Longfins were caught in June.  Baby Longfins should normally be seen sometime in March or April at latest.  According to Hobbs & Moyle (2015), young-of-year Longfins are rarely found when temperatures rise above 73 degrees F (22.8 degrees C).    

These tiny fish might indicate a disrupted late Longfin spawn in response to the recent winter dry spell with rain that finally arrived in March.  Hopefully, they are mature enough to survive the higher summertime temps.


Micah Bisson discovers Longfin Smelt #2 at Station UCoy2.

Longfins are designated as “threatened,” not yet endangered.  See “Saving the Longfin Smelt:”


Young Yellowfin Gobies from Pond A19.

Yellowfin Goby population boom.  Over 300, mostly baby fish, were caught each month in both May and June.


Roughly half the Yellowfin babies came from marshy Dump Slough alone in both months.  Yellowfin Goby populations seem to grow during drier years in Lower South Bay.  The recent relatively dry winter may have helped them recruit.   


Young Yellowfin Gobies from Dump Slough in the Photarium.


3. Tiny Fishes

Arrow Goby.  A total of 37 native Arrow Gobies and Cheekspot Gobies were caught in June.  These tiny (less than 2 inches long) fishes are very difficult to distinguish by eye.

Arrow Gobies have big mouths: the corner of the mouth (the maxilla) extends to a point well behind the eye.  This feature is much easier to see in the Photarium with macro lens photography.

Arrow Gobies tend to be found in, or near, warm shallow marshes and muddy bottoms.


Cheekspot Gobies have small mouths: corner of the maxilla terminates at a point in front of the eye.  Both the iridescent blue-black spot on the operculum (the “cheekspot”) and the small mouth are often hard to see. 

Cheekspots prefer deeper cooler water and hard substrate.     


Rainwater Killifish.  Only 24 Rainwater Killifish were caught in June.  I suppose that’s good news for this non-native invader.

Many of the 1270 species of Killifish around the world display some degree of sexual dimorphism (males and females have different appearance – males are generally more colorful).  Some varieties that are kept as aquarium pets are shockingly beautiful. 

Warning: shockingly beautiful killifish shown at this link:

Our variety, the Rainwater Killifish, is less colorful; olive drab overall.   Males are smaller and have more prominent dorsal and anal fins with a touch of black and red trim, respectively. 


4. Another Tire.

This old white wall was laying on the bottom at station Coy3.


5. The Worm!

Polychaete captured in Alviso Slough.

Neried Polychaete.  We usually find one or two Polychaetes each month.  I assume the muddy bottom of our Bay and sloughs is crawling with Polychaetes.  They are the preferred food for everything from ducks to Leopard Sharks.  


Neried Polychaetes are about the size and shape of terrestrial earthworms but more sophisticated.  These Polychaetes have eyes, palps, tentacles, and parapod legs (not true legs, but they function sort of like a combination of centipede legs plus gills). 


… THIS WORM HAS A BRAIN!  (not a true brain, but a “dorsal cerebral ganglion” behind the eyes.)  The animal can reason:  In less than a minute after we put this one in the Photarium, it oriented itself in the unnatural clear plastic trap under bright sunlight.  After it searched each corner using eyes, tentacles and palps, the worm deduced that UP was the way out!

We examine many species of fish and bugs in the Photarium: NONE are able to figure this out no matter how much time we give them.  But, the worm can solve the puzzle.  How amazing is that?


A worm with intelligence!


6. Striped Bass.

Striped Bass.  Ten Striped Bass were caught on the June weekend.  Eight were caught in May.  This represents a slight rebound, but so far, only 26 have been seen in 2020. 

We all used to love this non-native fish as our number one recreational sport fish in the Bay and Delta.  Nowadays, we don’t love it so much since it eats almost everything else.  Nonetheless, the stripers in May and June were looking well-fed and healthy, so that is a plus.


The biggest Stripers were caught at station Art1, immediately downstream from the San Jose/Santa Clara Regional Wastewater Facility.  The four fish ranged from 15 to 17 inches – standard length (to base of tail).  If we add the two-inch tails, at least two of the four were legal limit to take under California CDFW rules for Striped Bass (18-inch total length is the limit).


Tiny mysids clinging to clumps of bryozoan and plant material at station Art1.

We also encountered the highest density of Mysids, the best food for fish, here.  

I could again repeat the story about the beneficial environmental impact that results from this perpetual discharge of life-giving, tertiary-treated wastewater into this vibrant stretch of marsh … but you all have heard it before.


Fishing in Artesian Slough.

Two guys showed up to fish at station Art1 immediately after we had tossed our bass back in the slough.  This is where the fish grow biggest!  We have proof.

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