Fish in the Bay – June 2023, Is Summer here yet?

More baby fishes showed up in June!  This included 60 baby Longfin Smelt and 178 baby Starry Flounder which is unprecedented this late in the year.

However, total fish numbers dropped off considerably, which is completely normal for a June.  In most years, we call the warm months “Anchovy and Goby Season.” They are the main fish types that thrive in the upper marshes when waters warm and Dissolved Oxygen (DO) drops.

This year is a little different …


Water remained very fresh and DO was very high at all upstream stations.  This is good news for Longfin Smelt, but bad news for Anchovies.  We caught NO Anchovies at upstream stations.


Anchovies arrived to spawn upstream, but low salinity impedes them.  Only 49 Anchovies were seen downstream.  Individuals expressing eggs or milt were confirmed at each station. 

Goby counts remain somewhat low.

2023 is now already and officially our record Starry Flounder Year!  530 Starries have been caught since January.


1. Spring arrived late but was very intense.

Micah sacrificing the sprinkle donut on 3 June 2023.

Green vegetation erupted between May and June.  This was apparent from the very first trawl at Art1.  We were surrounded by greenness. 

Micah began the day with the donut sacrifice and traditional invocation:

“In the name of the river nymphs of the Alviso Marsh
To the naiads and dryads of Coyote Creek
To the gods; Poseidon, Triton, Neptune and Hercules (because we like him)
We make this offer of tasty treat in exchange for a safe day on the water and many native fishes.”

-J. Hobbs


Ulva – green algae.  We found two forms of Ulva during the June trawls.  The “Intestinalis” form at upstream stations looked shriveled up.  The “normal” form we usually see is leafy and diaphanous.**   

  • Ulva is also known as “Sea Lettuce.” It is highly edible. 
  • Ulva is a very common algae in LSB and around the world. We used to see piles of Ulva growing on the bare-naked mudflats of Pond A19 during summer months as recently as 2015.  Even today, our net often catches fragments of the stuff. 
  • Somehow, this very common plant-like organism has been mischaracterized and misunderstood for millennia: 

(** I call the leafy form “normal” because that is its usual appearance. Ulva species descriptions are confusing and have been corrected since the mid-2000s.  For example, “Intestinalis” is still described as a separate species of Ulva in many sources. But, recent research has concluded that Ulva just exhibits intestinalis form under certain conditions.)


Ulva has a strange alternating life cycle.

Ulva is NOT a plant!  It is a chlorophyte; a type of green algae that is more or less ancestral to the green land plants that are more familiar to us. 


String algae, aka filamentous algae.  We rarely see this nasty-looking green stringy stuff, but we found it in large abundance in Artesian Slough during June trawls.  All pieces we pulled up were crawling with amphipods and other bugs.   


String Algae was crawling with bugs (Corophium amphipods).


Striped Bass.  Only 4 Striped Bass were counted in June. 

  • Always remember, these brackish water barracudas are fast. We only catch young ones, and then only if they make a wrong turn. 
  • For better and for worse, these non-native fish had full bellies.


The green-pea soup of summer. The brackish marsh is highly productive. Greenness erupts in early summer in the local Coyote Creek tributaries: Alviso, Artesian, Dump Slough, Upper Coyote, and Pond A19. 

This is a perfect place to feed baby fish.


Tall dark green California bulrush at the water line in Dump Slough on Saturday.  White flowers of Lepidium (Pepper Grass) can be seen farther back.

California bulrush is blooming in all upstream sloughs.  It is the hardy tall, dark green native plant that grows in low salinity brackish water.  In fresher years, we see it growing far downstream.

  • These past three years of La Nina drought made the water salty and the bulrush scarce.
  • The big rains resurrected C. bulrush in many places where we have not seen it for years.


A lone stand of tall dark green California bulrush amongst a field of more salt-tolerant Alkali bulrush at Art3.

MARSH PLANT RULE OF THUMB #1: “Freshwater makes the marsh grow taller.”  This is because freshwater marsh plants organize themselves according to salt tolerance.  Freshwater rushes, sedges, and grasses generally grow taller than their more salt-tolerant cousins.

  • Cattails survive in nearly fresh water only. (Cattails are tall.)
  • California bulrush thrives in low-salinity brackish water. (California bulrush is also very tall.)
  • Alkali bulrush covers much of the marsh where salinity is higher. (Alkai bulrush is medium height.)
  • Spartina (Cordgrass) and Pickleweed live at the water’s edge in near marine salinity. Both of these can be regularly submersed in salt water and come out no worse for wear.
  • Cattails and California bulrush bounced back bigly after this recent wet rainy winter season.

MARSH PLANT RULE OF THUMB #2: Rushes have ridges; Sedges have edges; Grasses have round stems and hollow nodes.”

  • Micah taught me this rule. I do not yet fully understand it. But, it seems helpful.  We must understand marsh botany.
  • Bonus video describing Spartina alterniflora. (NOTE: alterniflora is the East Coast non-native spartina type, but notwithstanding that, it gives a good description of the Spartina lifestyle.) 


California bulrush is a very useful and edible plant.

California bulrush supports its own ecological community.  Bugs, fish, and birds live in it and depend on it. 


A patch of California Bulrush floating down Alviso Slough on Sunday.

Bulrush propagates like wildfire when the LSB sloughs freshen up.  Pieces of it break loose and seek new homes.


Another Tire at Coy1.  We deposited this one at the Alviso Marina waste bin. 


2. Fish that like freshwater.

Baby Longfin Smelt in June?!?!?  Longfins are a cool-water fish.  They ALWAYS flee to deeper water by June.  In over 10 years of trawling, we only ever caught three (3) Longfins in June 2020.  Other than that instance, NEVER! 

  • Good News! The baby-Longfin explosion continues, albeit it has tapered off a lot since May.  (60 baby Longfins were caught in June versus 1,184 in May.)
  • Bad News? Longfin fry this late near summer are much less likely to survive.  These fry should be bigger and gone by now.   Summer water temperatures are already in the low-20s.  This could be enough to give them ‘Longfin heat stroke.’ 


Longfin Smelt Spawning Ground.  From January through March, we found numerous adult male Longfins congregating in the cool freshwaters of Coyote Creek where it flows past Newby Island Landfill.  (A lone palm tree marks the spot.)

  • A few adult females were here as well, but females tend to stage several miles downstream in saltier water.
  • We presume that freshwater affects spawning Longfins much the same way as returning Salmon: spawning is likely an end-of-life suicide mission for the males.  
  • Females may make multiple trips to the Spawning Ground. We do not yet know if females live to spawn another season. 


In April, May, and now June, hundreds of baby Longfins showed up at all downstream stations! We have seen this spawning pattern each year for 3 or 4 years now.  But, we have never seen it so big and so clear. 


Pacific Herring. Five Herring showed up in June.  This was very late in the season for Herring. They are also almost always gone after May.

  • These Herring were brownish to greenish on their dorsal sides. Salinity at both stations was roughly 4 to 5 ppt.


Staghorn Sculpin eat shrimp, worms, amphipods, and baby gobies – pretty much anything that moves and looks tasty.  Sculpins have big mouths!

Warning! Staghorns have daggers over each operculum (their cheeks). You can cut yourself badly on a Staghorn’s horns if you grab them carelessly.  Getting stuck on their barbs can be painful. 


Staghorn Sculpin, one Starry Flounder, & many shrimp at Alv2

Young Staghorns are growing up.  These Sculpin hatched at the size of sesame seeds two or three months ago. 


Sacramento Sucker.  This is the only Sucker we have seen, since 2018 or 2019.  The wet rainy storm surge flushing pushes them downstream into our trawl area.  We only ever see very young and small ones. 


Starry Flounder Explosion.  The Year-to-date count is 530.  This already beats our previous record year of 2012 (465).  The runner-up year was 2017 (407).  There were many fewer Starries in all other years.

  • LSB data shows a strong correlation between rainwater flushing and baby Starry explosions. This is the biggest explosion ever! 


3. Some fish don’t like freshwater.

Two English Sole at LSB1.

English Sole count: 33.  The 2023 year-to-date count is 265.  Over 10 years the count has varied from zero (0) to a few thousand. These are the last English Sole we will likely see until after the next offshore hatch in December or January. 


California Halibut, LSB2

California Halibut count: 6.  Halibut both hatch and recruit in LSB, albeit most of them probably hatch in the deeper bay downstream.  Like so many other fishes here, they feed and grow on a diet of tiny bugs and baby fishes then eventually move downstream for bigger food.



Northern Anchovy count: 49!!!  This was the second-lowest Anchovy count for a June since 2017 when only 16 Anchovies were caught.  Anchovies don’t like the freshwater flush and subsequent low salinity. 

  • Anchovies come here to spawn in summer in the exact same locations where Longfin Smelt spawn in winter.
  • However, and most ironically, robust rainwater flushing encourages Longfin spawning and indirectly discourages Anchovy spawning.


As always, Anchovy dorsal color roughly correlates with water salinity: They “Blue-up” in salty water and Brown-down” as water gets fresher. The correlation is always strongest with Shad, intermediate with Herring and Sardines, and occasionally erratic in Anchovies.


Only 3 baby Leopard Sharks in June.  Freshwater has been keeping them away.  But, at least a few pregnant mamas delivered here last month. These babies are not more than a month old.


Bat Ray count = 3.  Rays move into LSB with the Leopard Sharks in summer.  They don’t like the freshwater either. 


4. Summer is (usually) Goby Season – Advanced Goby Identification Studies.

Goby Identification Key #1

Gobies are small but very charismatic fishes.  We regularly catch seven species: native- Arrow, Cheekspot, & Bay, and non-native – Yellowfin, Shokihaze, Shimofuri, & Chameleon.


Goby Identification Key #2 – Chameleon and Shimofuri Gobies

Don’t be fooled by Shimo/Chameleon body color.  Both species lighten and darken their brownish body color at will. 

  • As discussed in previous blogs, the light tan color pattern shows two dark longitudinal stipes along each side. We call that “Watermelon pattern” because it resembles the stripes on a melon. 
  • The dark brown color pattern sort of looks like snake scales, so we call it “Snakeskin color.”
  • Females and young of both species prefer “Watermelon pattern.”
  • Spawning-ready adults more often show “Snakeskin color.”
  • Spawning males of both species are documented as turning dark to near-black when they are attracting females and fighting off competing suitors.

In the example shown above, the Chameleons just happened to be in watermelon pattern.  The two Shimofuris were showing darker snakeskin.  Salinity was 18 to 19 ppt which is roughly the boundary for both species. 

  • Chameleons live in marine salinity. They don’t like salinity below 20 ppt. 
  • Shimofuri are brackish to freshwater gobies. They may visit, but will not remain long where salinity elevates above 20 ppt.     


Goby Identification Key #3 – Chameleon and Shimo dorsal and anal fin color.

Chameleon Gobies ALWAYS have a faint red stripe near the base of the second dorsal fin and anal fin. 

  • Chameleons have a white margin on both fins – but this is often very hard to see.
  • Shimofuris have an orange margin on both fins – but this can also be very faint especially when salinity is high and/or the fish is not in a spawning mood.


Goby Identification Key #4 – Chameleon and Shimo gobies continued


5. Bugs.

Crangon Shrimp count for June: 6,300.  Crangon numbers continue to look good. 


The 2023 year-to-date count is over 26,000.  This already exceeds total year counts from 2021 and 2022.  However, we have counted over 60,000 Crangon in a few good years.  We still have a long way to go.


Harris Mud Crab count – 8.  Male crabs are identified by narrow aprons on the dorsal side.  Female crabs have broad aprons that act as “trap door/escape hatch” – when the female expands with eggs, the apron opens to expose the eggs. 


Dead Eastern Mud Snail and Musculista shells at Alv2

More dead shells.  We continued to find some dead mud snail and Musculista shells in Lower Alviso Slough.  We presume this is continued aftermath from rainwater flushing earlier this year. 


6. Micro-world.

Janai Southworth joined us again during the June trawls.  Janai is the current president of the San Francisco Microscopical Society. 


Janai performed microscopic examination of samples collected on 4 June from each of the 10 downstream stations. 


We encountered floating scum-like material at station Coy4.  (Ordinarily, we assume that floating “cornflakes” might be cyanobacteria – possibly a bad thing!). 

Janai viewed samples using her EM1 Portable Field Microscope – and shared the view with us. 

  • We were stunned. The scummy surface material was largely composed of slowly gliding Pennate Diatoms.  We watched them slide around in real-time. 
  • This is a bottomless pit of living organisms. Who will ever sort out this complexity? If not us, Who?  If not now, When?  

** The above quote is not from “2001, A Space Odyssey” itself, “but from the novelization that screenwriter Arthur C. Clarke wrote at the same time as the screenplay. The book describes Bowman entering the star gate.  He says this before losing contact with Mission Control: “The thing’s hollow — it goes on forever — and — oh my God! — it’s full of stars!” 


Chaetoceros.  This is a very common type of centric Diatom – Janai found it at downstream stations.  The long filaments, called setae, are thought to be a defense against tiny fishes and/or a mechanism that slows the rate of sinking for these chains of linked organisms.   

  • “Due to its high growth rates, research has been conducted to potentially use of Chaetocerosin biotechnology.[2][7] Some Chaetoceros species are well-established commercial aquacultures.[8][9][10] Many of them are recognized as generally good producers of useful lipids and other biologically active products with high value-added. “
  • Chaetoceros is a primary producer. Who eats it?

Warning!  The proper way to pronounce Chaetoceros is something like “Kah-TAH-sor-ous.” (I used to call it “Chee-toh-sorous,” as if it was some kind of Cheetah–dinosaur hybrid.  That was incorrect!)


Bacillaria.  This is another common diatom in LSB. Clusters of several to dozens of them adhere to each other and glide back and forth like an extending ladder. 



Janai taught us about these two common and very similar-looking pennate diatoms:


A Stalked Ciliated at Alv2

Stalked Ciliates probably cover much of the benthic bottom biome.  But, we can only speculate.  Janai only spotted a few of them.

Stalked Ciliates are near the top of the microbial loop food chain.  Bacteria ‘eat’ the nutrients (C and N). Stalked Ciliates eat the bacteria.  Swimming Ciliates, like Paramecium and tintinnids, along with some Dinoflagellates and Euglenids are all members of this first consumer trophic brigade.     

  • In the sewage treatment profession, Stalked Ciliates live in mature sewage sludge. They are a sign that 1) carbonaceous material has been largely absorbed into filamentous bacteria, and 2) that nitrogenous waste (Organic N, NH3, and NO3) have also been largely absorbed into NOA and NOB bacteria.
  • Stalked Ciliates can tell us that nutrients are being well digested (e.g. removed from the water column).  
  • Stalked Ciliated must also be eaten. All living creatures eat and are eaten.


A rotifer at Alv3.  – Note the bright red eye.

Rotifers are also remorseless eaters.  Many small fishes eat rotifers.


A dark field microscope view of the micro scene at Coy4.

Copepod nauplii are among the most important foods for small fishes.

The importance of Copepods as baby fish food is well-known amongst aquarium hobbyists.


Copepod nauplii at Coy4 in June.

The darkfield microscope view highlights the appealing deliciousness of these organisms. 


Three generations of a Copepod family from Coy4 – bright field microscope view.

Copepods graze food from the top of the “microbial loop.” 

  • Numerous studies suggest that Copepod abundance can exert profound influence over nutrient cycling at the microbial level. – e.g Tsagaraki et al. (2018)
  • Absent copepods, most carbon and nitrogen would remain unavailable to larger animals like fish, birds, and ourselves.
  • They say that the total biomass of copepods in the world greatly outweighs the biomass of all other animals – from the tiniest insects to humans and all bigger creatures.


Adult Copepods from Pond A21. 


Moby – The Perfect Life (Live at The Fonda, L.A.)

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