Fish in the Bay – Boy’s Town / Girl’s Town – June 2026.

We returned to Lower South Bay (LSB) for June trawls.  This was a relatively relaxed month with only two days of trawling: LSB upstream (Coyote Creek and sloughs upstream of the railroad bridge, and LSB downstream (Alviso Slough, the mouth of Coyote Creek, and Lower South Bay proper). 

LSB Fish numbers improved in June.  This was largely due to a big influx of girl Anchovies that migrated far upstream.  This happens every summer, but we didn’t really understand it until recently.  We started to notice a boy/girl trend around 2023.

• The SF Bay population of Anchovies migrates to upstream marshes to spawn in the warm season.  It’s mainly the girls who do this. 
• Girl Anchovies swim into warm, brackish (and even severely anoxic) marshes in search of protein to feed their growing egg-masses. 
• Boy Anchovies tend to loiter in cooler, deeper Bay water.  Observations since then, continue to confirm it.  Boy Anchovies, with less body burden, have no need to take such risks.  Boys generally wait in the cool deep Bay.  They know the girls will return when their eggs are ready (roughly once per week).

At downstream stations, we generally saw the same Anchovy boy/girl division: Boys outnumbered girls at LSB1, LSB2 and Coy3; Girls were more numerous everywhere else.    

Good News:

• There were many Yellowfin and Cheekspot Gobies, and
• Lots of young Halibut, a couple of Tonguefish and a Croaker.  Warm water El Nino fishes continue to present themselves.

Bad News: 

• Non-native Corbula clams continue to show up in very high numbers.
• Non-native Philine snails exploded at LSB stations.
• Shrimp and Eastern Mud Snail numbers have fallen to near historic lows.  We can’t help thinking that this could be a result from the ongoing Corbula explosion!

1. The New Boat & Artesian Slough.

The new boat, Dr. Hobbs, Alex Lama, and Alan Aguilar (behind Hobbs) at Art1 on 25 June 2026.

A new boat, the “Longsme 2,” was used to perform trawls in June.  This new boat is a little shorter, and arguably a little better engineered, than the original “Longsme” boat that has been in service since at least … 2017(?)  

• UC Davis monitoring workload increased greatly with new Wetland Regional Monitoring Program (WRMP) trawls at Bair Island, Eden Landing & various places in San Pablo Bay / North Bay. 
• A single trawling boat was no longer sufficient.  The original “Longsme” boat will also remain in service for some years to come.

Artesian Slough – Upstream (station Art1)

Artesian Slough upstream (station Art1) as viewed from the boat launch next to the discharge from the San Jose-Santa Clara Regional Wastewater Facility.   

• On almost any clear, calm morning, Artesian Slough presents itself as a near perfect “reflecting pool.”  No expensive liners or fancy paints are needed. 
• Beneficial biological processes maintain this pristine look. 
  • Marsh plants grow tallest here: Cattails and California Bulrush stand taller than an elephant’s eye when water is consistently fresh enough.  Tiny aquatic bugs are dense.  Fish feed on the bugs.  
  • Female Anchovies seek abundant food here in summer.  Longfin Smelt girls do the same in winter.   
  • Herons, Egrets, and marsh wrens’ nests are dense along the shores.  Terns and Pelicans occasionally drop by for the feast.

Art3 (Artesian Slough – downstream)

Around 1.5 miles downstream from the Art1 “Reflecting Pool” experience, the waters of Artesian Slough ‘brown down” to a murky shade of “Antiquity” or perhaps “Melange Green” on the Sherwin-Williams color scale. 

• This color change and increase in turbidity is entirely natural: A beneficial consequence of tidally resuspended sediments and phytoplankton growth.

Small side-note regarding birds.  A bonded pair of California Gulls were perched on the hydraulic intake structure to pond A18 as we motored past. They softly muttered to each other in sounds entirely different from typical gull calls. They conversed in soft squawks back and forth between them.  The pair was clearly squawking about us as we made our closest approach. 

• Listen carefully!  Bonded boy-girl bird pairs ‘talk’ to each other in a different tone.  Falconers first recognized this bird language centuries ago.  It’s called E-chupping.  Many different bird species do this. It is a sort of romantic “baby talk” that bird partners engage in.  Once you hear it, you will never unhear it.
  • “E-chupping” is a specific, soft, and rapid vocalization made by peregrine falcons to communicate with their mates. It sounds like a repeating “eeeee-chup” and is primarily used during courtship, to encourage a mate during nest exchanges, or just prior to the male bringing food to the female.”
• Don’t imitate birds when you hear this! – Pay attention and learn.  If the birds are looking at you during E-chup conversation, they are likely talking about you: discussing the potential danger FROM YOU.  They may go silent, or abruptly flee, if you try to mimic them.  (How would you react if a nearby lion, tiger, or bear started imitating your own private conversations with your partner?)  – You learn nothing if the birds stop talking! 

2. Interesting Fishes.

Striped Bass count = 4 / year-to-date = 14.  2026 remains our lowest Striped Bass year on record. 

• Stripers can die of heat stress when water temperatures exceed 25 degrees C.  It’s one reason why big adults avoid upstream marshes in summer. 
• Already, late June 2026 temps in Dump Slough and at Upper Coyote stations are near, or over, the high temp limit for Stripers.

Anchovy count = 531 / year-to-date = 1249.  Anchovy numbers bumped up substantially in June.  They appear to be almost entirely young adults with some young-of-year mixed in.  The vast majority measured 70 mm or less. 

• We confirmed only 8 males in the upstream bunch of over 400 on June 25^th.
• In contrast, we observed over 20 males the following downstream day in an over-all population of only 117.
• We have seen this same Anchovy “males downstream / females upstream” skew over the past few summers.  It is a real phenomenon, albeit our sampling techniques have not always been rigorous.  We simply squeeze some Anchovy bellies to see if eggs or milt are present before releasing them. 
  • A more complete scientific approach would require slicing open all Anchovy bellies to evaluate the reproduction state of their gonads.  … (Potentially 100% sacrifice!) 
• • How important is this Anchovy boy/girl information?  The value of the information must exceed any sacrifice of Anchovy lives.  
  • For now, we are content with our kinder, gentler approach.

Halibut count = 80 / year-to-date = 232.  This was our highest monthly Halibut count since March 2016 at the tail-end of the big ‘quasi-double’ El Nino of 2014-16.

• Halibut are yet another marine fish that migrate farther upstream in the marshes than most people would imagine.  For Halibut, it is all about juvenile recruitment.  Big Halibut mamas deposit fertile eggs as far upstream as they dare go during the cold months.  Hatchlings either swim or drift farther upstream to brackish waters.    
• Baby Halibut eat roughly the same food as Anchovies: tiny bugs like Mysids and Amphipods.  A major difference is that Halibut switch to eating Anchovies as they grow bigger.

Bay Goby count = 1 / year-to-date = 29.   For no apparent reason, 2026 is one of our best Bay Goby year on record.  Only years 2020 and 2021 were better with 31 and 33 Bay Gobies respectively.

• This is the first adult-sized Bay Goby we have seen in LSB in almost a decade!  Three to seven dark bands (dashes) along the lateral line and short jaw (maxilla ends in front of the eye) are key field identifiers.
• Native Bay Gobies were the most numerous mid-sized gobies in LSB at least through the 1980s.  They have been rare to non-existent since the UC Davis team started monitoring here in 2010.

Leopard Shark count = 3 / year-to-date = 6.  The Leopard Shark total remains low, but it is still early in the year. 

Another boy/girl skew.  Both literature and our own observations confirm that the elasmobranchs we find here in LSB, Leopard Sharks, Guitarfish, and Bat Rays, follow the same general rule: 

• Boys loiter in cooler deeper waters downstream.
• Girls brave the warmer, shallower, and less salty marsh waters to give live-birth to pups. 

This fundamental rule of marsh ecology affects the life cycles of many different unrelated fish species.

• Girl fishes, their eggs, and their babies need abundant food that grows in turbulent dangerous places where rainwaters deposit nutrients and cultivate the bugs.  
• Boy fishes generally have no need to expose themselves to the additional risk. They wait downstream knowing that the girls must return.    

Alan Aguilar & Alex Lama examining young Bat Rays.

Bat Ray count = 12 / year-to-date = 20.  All Rays were young-of-year, probably born in the late warm days of 2025. 
 

Every fish tells a story.  But, what sense can we make of the oddballs, the outliers?

Longjaw Mudsucker count = 20 / year-to-date = 49.  Eighteen Mudsuckers were caught in restored Pond A19.  Suddenly our Mudsucker count jumped to the highest since 2022.  What does it mean?

White Croaker count = 1 / year-to-date =12.  2026 now stands as our record Croaker year.  Personally, I want to believe that Croakers, and the broader family of Drums, are indicators of warm sea surface temperatures in the Pacific.  But honestly, twelve fish over the year mean absolutely nothing!  Our next highest Croaker year was ten in 2021 which was a La Nina year!   Croaker abundance in LSB seems to be entirely random at this point.

California Tonguefish count = 2 / year-to-date =61.  Yes, the Tonguefish count means something.  We have not seen so many Tonguefish in LSB since El Nino in 2015 and 2016.  Tonguefish are a quintessential El Nino fish for us!

Dr. Hobbs in his dream car.  We found a toy model Chevy Silverado Z71 exposed at low tide at upstream station WSM1.  Hobbs hopes to own a full-scale truck like this someday.  This toy car would have been a prized trophy for Hobbs’s backyard garden.  Unfortunately, the tiny pickup was chockablock full of mud and weighed at least 300 pounds. Recovery was not an option.  We will return to collect it someday in the future.     

3. Bugs & Bryo-balls.

485 Palaemon and 163 Crangon shrimp at station Alv3 on 26 June 2026.

This place is usually a “shrimp hotspot,” but not so much this June:  Shrimp populations in 2026 are running close to 1/10^th the 2018-to-2025 average. 

• The last time we saw Palaemon and Crangon shrimp numbers roughly this low was in 2015-to-2016.  Hence, it is possible that low shrimp numbers result from El Nino and warm sea surface temperatures offshore. 
• On the other hand, excess Corbula clams this year are likely sucking up significant amounts of microscopic food. 
• Investigation continues!

Tiny Bugs are fundamental to the health of this ecosystem.  Our trawling methods are crude, and we can only measure what we can see.  Generally, one centimeter (10 mm) is our lowest level of bug detection.

Amphipod count = 2469.   Most of these bugs were counted in Artesian Slough. 

• The bugs in Artesian slough were definitely Americorophium spinicorne  https://scholarsbank.uoregon.edu/server/api/core/bitstreams/7a6a3619-fd05-4a8d-a2f4-71d96a0a3898/content 
• Farther downstream, Amphipods in Pond A21 looked and behaved entirely differently; they were faster swimmers with much shorter antennae.

Mysid count = 686.  Most Mysids were caught at upstream stations. 

Marine Flatworm count =1 at Art1.   Alex Lama discovered this marine flatworm at station Art1.  Flatworms tend to be small and very hard to see.  Alex has a special ability to find these cryptic creatures.

Philine snail count = 1547 / year-to-date = 1554.  What the heck happened here!?!?!  Suddenly, these nasty, slimy, non-native, snotball snails exploded at LSB stations. 

• We have observed Philine snails since at least 2016: a few dozen to several hundred in any given year. 
• We never counted more than 500 in any year until now. – What does it mean?   

Corbula Clam count = 5,121 / year-to-date = 30,970. 

• Good news: Corbula numbers are down by half.  Last year at this time, we counted over 53,000.  
• Bad news: Aside from last year, this is still the highest Corbula count on record, – by far. 

Bryo-balls at Alv1 on 26 June 2026.

Bryo-balls!!!  We haven’t figured out a good way to quantify “Mossy Bryozoan” colonies.  They form stiff but soft colonies of many thousands of individual “zoids.”  Spongy zoid colonies are analogous to polyps in soft corals. Zoids filter creek water from rainwater flushing. The overall texture of “bryo-ball” colonies is similar to brillo pads.

• We find Mossy Bryozoan “bryo-balls” near the mouths of the healthiest river and creek systems.  Bryo-balls perform some important aspect of biological nutrient filtration; we are just not yet sure exactly what and how much.     

4. Water Colors.

Water Colors half-way between first quarter and full moon.  During June trawls, the Moon was ‘waxing Gibbous.’  This was midway after first quarter (1Q/neap tide) and a few days before Full Moon (F/spring tide). 

• We observed a brief period of high turbidity brownness at LSB1 just before slack high tide near noon.
• We are confident that these local marshes in LSB are completely immune to fish-killing red tides.  Nonetheless, we carefully monitor water colors just in case.