Fish in the Bay – June 2025, Return to Lower South Bay (LSB).

After several visits to San Pablo Bay in the north, we returned to Lower South Bay marshes in early June.  It was good to be back home again. 

We last left this southern portion of the Bay in the middle of a Corbula Clam crisis.  The nasty Clam’s monthly count peaked at a record 26,155 in May!  Encouragingly, Corbula numbers in June dropped to “merely” 5,894.  (The June count is still huge – by itself, it would be our largest monthly count since 2012.)

• To better understand this year’s Corbula explosion, we continued recordiing measurements of the largest clam at each station – see notes at bottom of each spreadsheet.  This month’s clam study is discussed in greater detail below.

Spawning Anchovies!  The summer Anchovy count is climbing.  Egg and milt bearing fish were found at almost all stations.

Baby/Unidentified Goby counts were high again – 453.  Was this an extra – extra baby fish month in June?  Who were these extra baby Gobies after April? 

• June totals yielded possible clues: Yellowfins increased from 68 in May to 414 in June; Arrows increased from 4 to 33, and Cheekspots from zero to 493.
• These newest unidentified babies are probably Cheekspots with some Yellowfins mixed in! 

1. Summertime Marshes.

Top image: Research Vessel Triplett and the new City of San Jose crew at Art1
Bottom images: Marsh Wren nests in tall bulrush farther downstream.

We encountered the City of San Jose Environmental Compliance team as we launched on June 11^th.

• I recognize the boat, San Jose’s RV Triplett, but I don’t recognize the young faces anymore. Some of these new people are members of the same group I retired from in early 2018. … People like us come and go.  Marsh wetlands recover and endure when we let them.
• There was no time for pleasantries.  Both our teams had several ecosystems to examine and only limited hours to do the job!

Constant flow of fresh water in Artesian Slough makes marsh plants grow tallest here.’  – Look at the size of those bulrushes!!!

Additional WRMP stations in Pond A17 and Warm Springs Marsh (WSM) expand our observations of marsh restoration in this area.  Each pond or marsh segment was opened to tidal flows in recent decades.  Recovery of tidal marsh requires time for sediment deposition and marsh plant colonization. 

Pond A17, ultimately opened to tidal flow in 2013, is now crossing a threshold.  Spartina and bulrush are just starting to spread across the pond.

Pond A19, breached in 2006, is close to 80 percent covered with Spartina and bulrushes. Sediment deposition was slow for most of the early years, hence full recovery has taken almost 20 years.

Pond A21, also breached in 2006, restored faster than anyone predicted.  Sediment deposited very quickly at this location.  Pond A21 has hosted a dense garden of Spartina, bulrush, and Pickleweed for longer than we can remember now.  … 10 years for full recovery?

Pond A12, remains a salt pond with minimal circulation.  Compare and contrast this barren wasteland to the previous examples. Imagine how this pond would look now had it been opened to tidal flows almost 20 years ago!    

• Admittedly, some people see beauty in the Pond A12 ongoing ecological disaster.
  • Why is the A12 pond pink?
    https://parks.santaclaracounty.gov/locations/alviso-marina-county-park/A12 

Warm Springs Marsh (WSM) is an unusual place.  This far upstream marsh was opened to creek and tidal flows decades earlier in 1988.  Tall bulrushes fringe most of the area, but the center is dominated by a large, denuded mudflat.  The mudflat serves as a roosting place for California Gulls and American White Pelicans. 

• We do not see any similar mudflats near here.  Do stomping feet of roosting birds sustain this muddy landscape? 

Interesting observations.

1. On weekdays, a cloud of California Gulls hovers over garbage processing at the top of Newby Island Landfill.  Many of the gulls took notice of us as we trawled WSM on June 11^th.  We soon had a small cloud of gulls soaring over us.  It was an impressive sight!
   
2. Meanwhile, at the mudflat … a group of 30-to-40 American White Pelicans staked out an area amidst the horde of roosting gulls. They must be here for food.
   1. Pelicans are “big bully birds.”  They will eagerly steal food from smaller gulls, and they even occasionally swallow smaller birds whole when they are really hungry!
      
3. The WSM station is the only place where we reliably find chicken bones in our trawl catch. Protein flows from the landfill via gulls … and to some extent to big bully Pelicans.

Warm Springs Marsh also supports aquatic life.  Some fish species need this lower-salinity tidal marsh along Coyote Creek.  This native Sacramento Sucker is another prime example. 

• What a beauty he/she is!

2. Bottom Dwelling Bugs.

Amphipod count = 7,382. (all but 1,000 were at upstream stations)

Amphipods = low salinity.  High Amphipod counts correlated with a strangely pleasant-feeling fluffy clumpy mud at upstream stations in June. 

• Soil texture at stations Art1 thru Art3, Alv1, & WSM1 was noticeably different than anywhere else.  It was not coarse-grained-to-sandy as we see downstream near LSB; not dense brown and sticky as is typical farther upstream in sloughs.  And, it was not black, oily, and sulfur-smelling as usually found in Pond A21 borrow ditches (a product of anaerobic sulfur-reducing bacteria).
• This different dirt had a slightly fibrous structure and no stickiness at all.  It was also crawling with Amphipods (Corophium and Ampilesca Gammarids) everywhere we found it.

Amphipods are tiny bugs.  They measure between just a few-to-several millimeters.  They are so small that they can be hard to see at first. We often first detect them from the wiggling sensation against our skin. (Once you recognize the creatures, the feeling is somewhat soothing.)   

Is this fluffy soil Amphipod Poop?  Wastewater treatment professionals will immediately recognize this fluffy floccular material as processed material from microscopic organisms.  Amphipod poop + amphipod silk?

• Some crustaceans have evolved a way to make silk – Gaining and losing that ability fueled great diversity in one group called amphipods (2024) https://www.science.org/content/article/some-crustaceans-have-evolved-way-make-silk
  “The creatures make silk for different purposes. A few use it to bind sand grains and poop, sometimes to make soft, protective tubes in the mud, or hard tubes through which they pump water to collect food.
  
• Kronenberger et al (2012) A Novel Marine Silk.
  “The tube-building corophioid amphipod, Crassicorophium bonellii, produces from its legs fibrous, adhesive underwater threads that combine barnacle cement biology with aspects of spider silk thread extrusion spinning.”

Amphipods are extremely beneficial bugs!  This is good poop.

Corbula clam count = 5,894.  This was a sharp reduction from the ~ 20k Corbula clams we counted in April and May.  Nonetheless, 5,000+ is still an alarmingly high monthly count here.

We again measured individual sizes of clams in June.  Due to time constraints, only the largest clam in each batch was measured using a micrometer wrench.  It was not an ideal solution, but better than nothing.

Clams at station Art3 in June were again generally larger than those found at any other station on the upstream side.  Clams at UCoy2 were next in size on average.  (A single large 25 mm clam measured at station UCoy1 was an extreme outlier.  All other Corbula at that station were a few to several millimeters smaller.)   

• This suggests that a Corbula “sweet-spot” for maximum growth and reproduction exists along Coyote Creek between stations UCoy2 and Art3.

Corbula measurements at downstream stations yielded a similar trend: The largest Corbula clams were found at station Alv1.  Clam sizes decreased steadily with increasing salinity and downstream distance. 

Interesting Observations.

• Corbula clams were bigger and also browner and crustier at upstream stations.  Clams were progressively smaller, shinier, and presumably younger, with increasing distance downstream.
• Most Corbula at downstream stations had huge barnacles growing on them.  (Juvenile barnacles anchor to hard substrate when they settle.  Unlike other local clams, Corbula live partially exposed on the benthic surface.)
  • These results suggest that barnacles alone may inhibit Corbula growth where salinity is consistently above ~ 10 ppt (?) in LSB!  

Harris Mud Crab count = 7.  Non-native Harris crabs inhabit upstream brackish marshes.  Females are usually brooding eggs during warm season.

Dungeness Crab count = 4.  Young Dungeness Crabs drift in from the ocean.  Only young ‘Dungees’ show up in LSB.   

Oregon Mud Crab count = 1.  Oregon Mud Crabs, a.k.a. Yellow Shore Crabs, are usually found in saltier water downstream. 

3. Water Colors.

In June, we trawled during Full Moon (Spring Tide). Outside of a couple of upstream stations, water color was a near uniform highly-turbid shade of “Different Gold.”

• Red Tide Season is fast approaching.  We are keeping our eyes on the water.  

H. akashiwo is a microscopic “phytoplankton.” This particular Raphidophyte (https://en.wikipedia.org/wiki/Raphidophyte) caused the fish-killing red tide in central SF Bay three years ago in July/August of 2022.

• Populations of tiny H. akashiwo organisms can explode into a dark red or brown blooms in late summer when temperatures are high and the water column is calm and highly stratified.  (The highest risk of H. akashiwo bloom is during neap tides with still winds.)     

4. Sharks & Rays.

Leopard Shark count = 9. Nine baby sharks were caught at station Coy4.  Standard lengths varied; half were small and half were longer.  These babies must have come from at least two different litters.

Baby Bat Ray at Coy4

Bat Ray count = 10.  All ten Bat Rays in June were babies.  Wingspans ranged from 160 to 260 mm (up to 10 inches).

5. Gobies & Sculpins.

Cheekspot Goby count = 493.  We saw a similar surge in small Arrow/Cheekspot Gobies in June of 2022.  Unfortunately, these two native gobies are difficult to tell apart under field conditions.  (In 2022, we were not yet reliably distinguishing Arrows from Cheekspots.) 

• This time, we are confident that this latest surge is overwhelmingly composed of Cheekspots.  

More young gobies at stations Coy1 and Coy3. 

Yellowfin Goby count = 414.  Young Yellowfins are the other product from the ‘Extra Baby Fish Month’ we witnessed in May. 

Staghorn Sculpin count = 90.  The Staghorn count dropped after surges of young ones in April (484) and May (288).  Expect to see progressively fewer Staghorns each month until the next spawn in February and March.

Prickly Sculpin count = 7.  Pricklies migrate downstream to spawn in brackish waters.  Their numbers tend to peak in April through June. 

• Big rainwater flushes = More Pricklies.  Our record years for Pricklies were 2017 (406) and 2019 (309).  In other years, we caught as few as only one (1) and up to as many as 57.    

Unidentified / Baby Goby count = 453.  This was a third consecutive high “Baby Fish” count for this spring/early summer season!  As explained above, we suspect that many of these late-arriving babies continue to be Cheekspots. 

Longjaw Mudsucker count = 3.  We have seen NO Mudsuckers in 2025 until now. 

Shimofuri & Shokihaze Goby counts = 9 & 9.  The Shimo/Shoki score was tied in June. 

• If ENSO has some kind of indirect affect on these two fishes, the coming La Nina may boost Shimofuri recruitment with coinciding decline in Shokihaze numbers.  Time will tell.

6. Spawning Anchovies.

Anchovy count = 259.  Anchovies are migrating into Lower South Bay right on schedule.  The count jumped from 52 in May to 259 in June.  Limited “egg checks” confirmed that these Anchovies are once again in a high state of spawning readiness.

• We are also finding: 
  • More egg-bearing Anchovies upstream in restored ponds and sloughs, and   
  • More milt-bearing males at downstream stations, i.e. Coy4, LSB1 and LSB2.

In addition to the downstream male/upstream female distributional split, measurements over recent years also confirm that Anchovies are smaller on average at far downstream stations (Coy4, LSB1, & LSB2).  They tend to be bigger in upstream ponds and sloughs.

• Photos above are roughly matched in scale to illustrate size differences between upstream (girl) Anchovies, at left, and downstream (boy) Anchovies, at right. 
• Food availability continues to be the likely explanation.  Big female Anchovies must consume enormous amounts of protein to support development of multiple batches of eggs throughout the season.  Males probably enjoy literally “chilling out” in cooler, saltier downstream waters – unless they get really hungry.

7. Flatfishes.

Starry Flounder count = 11.  All starries were babies.  The year-to-date count is 32. 
 

California Halibut count = 25.  We are catching a pretty good number of young Halibut.  2025 is already our 4^th best year on record.  Half the calendar year is still ahead of us!

The Anchovy story reminds me of an old Billy Joel tune.  The song is now stuck in my head.

Billy Joel – Uptown Girl (Official Audio) https://www.youtube.com/watch?v=o-0Oect0nVQ&list=RDo-0Oect0nVQ&start_radio=1