Fish in the Bay – North Bay.  July/Aug 2026.

August 29, 2026 Jim Ervin
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Fieldwork, Fish in Lower South Bay, News

We trawled San Pablo Bay (aka “North Bay”) in the later weeks of July and August.  The map above summarizes the four trawl areas: Napa, Petaluma, Gallinas-Hamilton, and Wildcat along with box scores showing some of the fish and bug tallies.

  • What do the numbers mean?  This is the second year of fish monitoring in North Bay under the Wetlands Regional Monitoring Program (WRMP).  https://www.wrmp.org/  We can compare and contrast 2025 numbers against this current year, but beyond that, the short history in the north makes it still difficult to assess long-term trends. This is particularly vexing during a potentially “once in a generation” El Nino. Overall fish numbers (aside form Halibut) seem low and probably are. 
  • In contrast, we have over 14 years of data from monthly trawls in LSB. For that reason, I will be making a lot of comparisons between North Bay and LSB numbers to try to build a long-term picture out of the limited data so far.    

1. Baby Fish Month in July?

There was a sharp increase in Yellowfin, Arrow, and Cheekspot Goby counts in July.  We saw the goby surge in Wildcat, Gallinas-Hamilton, and Petaluma. (But NOT in Napa).

  • Yellowfin Goby count in July = 377.  (versus 182 in LSB)
  • Arrow Goby count in July = 72.  (versus 77 in LSB)
  • Cheekspot Goby count in July = 1,413!  (versus 43 in LSB)
  • All gobies were tiny.  Almost all were between 20 to 40 mm in length.  Gobies listed as “Unidentified” were smaller at around 12 to 20 mm.  (For comparison, in 14 years of monitoring in LSB, we have only seen comparably high goby numbers in May, June, and July of 2022.  Numbers are much lower this current year.)
    • Always consider Catch Per Unit Effort (CPUE).  We conduct 5-minute trawls in North and upper South Bay versus 10-minute trawls in Lower South Bay (LSB).  In theory, each catch number from North Bay should be doubled for fair comparison with LSB. 
      • BUT, also consider that a total of 42 stations are trawled in North Bay versus only 20 in LSB.  Therefore, the overall trawling effort is roughly equal.
      • If we drill down further into specific areas or river systems, the numbers get more informative:  almost ZERO gobies were caught in 12 stations in the Napa river system versus almost 1,100 Cheekspots alone from 10 stations along the Gallinas-Hamilton shore.  

Baby Fish Month? – or is it a season?  For years, we recorded hundreds of baby gobies during “Baby Fish Months” around April or May in warmer and more protected Lower South Bay.  Dr. Hobbs suspects that abundant rain patterns along the Gallinas and Petaluma shores stimulate “Baby Fish Month” in North Bay / San Pablo Bay perhaps a few months later than what we typically observe in Lower South Bay.   

Shokihaze Goby count = 67 in July / 2 in August.  (In LSB we caught 1 Shoki in July and 2 in August.)

Shokihazes also contributed to the July “Baby Fish Month” count in North Bay.  But, unlike the other gobies, Shokis were almost exclusively found in Petaluma River.  We see this consistently: for some reason, Petaluma River is a Shokihaze haven. 

Maybe, the Petaluma River river system has simply not yet been invaded by Shimofuri Gobies – the main rivals of Shokihazes.  Or perhaps Petaluma River is simply more Shoki-friendly for other reasons. 

Prickly Sculpin count = 2 in July / 1 in August.  The three were caught in Napa; specifically near Pond 2 and Nap1 stations. 

Another mystery:  We find almost all Pricklys exclusively in the Napa River system.  The 2026 year-to-date count is 12 in Napa, 1 in Petaluma, 2 in LSB, and zero everywhere else. 

(In some previous years, like 2017 and 2019, we caught many more Pricklys in LSB.  But the number is highly variable and seemingly dependent on rainwater flushing.  Prickly numbers dropped to less than 20 in LSB in 2024 and 2025.  And now to near zero for 2026.) 

Napa is the Prickly capital of North San Francisco Bay!  But why?  Native Pricklys depend on good connection between freshwater creeks and saltier bay water downstream.  Something near stations P2A1 and Nap1 seems to provide that connection even during this otherwise poor Prickly year. 

2. Clupeiformes.

Anchovy count = 234 in July / 103 in Aug.  (versus LSB counts of 172 / 118)

Herring count = 29 (58) in July / 0 in Aug.  (versus LSB counts of zero in both months)

Shad count = 0 in July / 113 in Aug.  (versus LSB counts of zero)

Clupeiformes are small silvery pelagic fishes that big creatures like to eat.  They are also among the first fish populations that crash during a big El Nino. In LSB, we are experiencing a bad Clupeiforme year so far: counts of Anchovies, Herring and Shad have almost bottomed out for the 14-year LSB record.  In contrast, Anchovies might be doing a little better the Wildcat, Gallinas-Hamilton, and Petaluma areas.  Herring and Shad are wintertime fishes in the LSB, so we were surprised to see them show up out of season in North Bay..    

  • Tentatively, the Gallinas-Hamilton shores again stand out as havens for small fishes in North Bay.  The Wildcat embayment is close second.     

Like most fishes, Clupeiformes swim in schools.  Sometimes, a big jump in numbers is just a matter of luckily trawling through a school.  For example, 88 of the 113 American Shad caught in August were caught at just one station in Miller Creek.    

It was interesting to see such a large number of uniformly young Shad all at once.  Their dorsal colors were blue-green shads between “Thermal Spring” and “Jadite” which was roughly consistent with salinity around 23 to 24 ppt. 

… As always, their sides were silvery mirrors.  The same guanine crystals produce dorsal color also the silver mirror sides.  But, the crystals are arranged differently.  Dorsum crystals refract a wider range of colors.  Crystals in side scales mostly reflect. 

Shad Glitter:  All Clupeiforms shed some side scales when they are disturbed.  It is part of their camouflage defense.  Some scales drop off as the fish thrash and flee.  The cloud of lose scales dazzles and confuses any predator. 

After the 88 Shad were counted and released, a small pile of glittery scales remained in the measuring tray.  In bright sunlight, we could clearly see shades of violet and blue refracting from the detached scales. 

We learned years ago that Clupeiforme dorsal sides “blue up” in high salinity (generally above around 20 ppt) and they “brown down” in fresher water (below roughly 10 ppt). 

  • This time, it immediately dawned on us that blue and violet colors we were seeing in the side scales might also “brown down” if we add fresh water, so that is what we did.
  • Salty ambient water was decanted off and replaced with fresh drinking water (0 ppt) at 10:41 AM.  Within 3 minutes all traces of blue and violet disappeared from the scales!
  • A few minutes later, we decanted off the fresh water and replaced it with ambient salt water (23.7 ppt).  It took just a little longer, roughly 4 minutes, until the blue and violet colors returned. 

Great Scott!  These are dead scales.  It is as if our own fingernails or hair could change color back and forth in response to the environment!  Just to be sure, we repeated the experiment on two more occasions when we caught more Shad during the week.  The result was the same, albeit blue and violet do appear to fade a bit with each successive test.  And when scales were allowed to completely dry out / desiccate, the colors vanished permanently. Rehydration does not bring the colors back.

Once you see the color, you can never un-see it.  We had long noticed that the entire body of a Clupeiforme seems to be bluer in salty water, not just the dorsum.  But it was, and is, a subtle effect.  Maybe, our eyes were fooling us … Maybe it was the reflection of the blue sky … so we used to think.

Now we know.  Blue and violet are baked into the silvery sides when salinity is high.  It is subtle: the colors are constructed from refraction.  At some angles, blue and/or violet hit our eyes.  At other angles, all we see is silver.  The faint colors shift and shimmer, from blue to violet to silver, as the fish moves through the water.   Unbelievable!

Pay close attention to the silvery sides.  What colors do you see?

3. Flatfishes & Bat Rays.

Halibut count = 42 in July / 8 in Aug.    Comparable Halibut counts in LSB for July & August were 32 & 23.   The longer record in LSB shows that this 2026 El Nino is a bumper/high year for Halibut.  North Bay had a few more Halibut in July but fewer in August. 

  • Overall, the numbers confirm that El Nino Halibut recruitment is a Bay-wide phenomenon. 

Starry Flounder count = 6 in July / 1 in Aug.  Comparable numbers in LSB for July and August = ZERO. 

2026 is the worst year for Starries in 14 years of record for LSB.   This is a bit ironic because 2023 was our best year in LSB.  At least the limited Starry catch in North Bay this year makes up for some of the Starry deficit in the south. 

Bat Ray count = 5 in July / 1 in August. ( LSB numbers were Zero and 4.) 

Bat Rays eat small gobies.  The Bat Ray count was low but generally consistent with the surge of baby fishes in the Gallinas-Hamilton and Petaluma areas.   

4. Bugs. 

Most invertebrates we find in the Bay are non-native.  The table above shows the North Bay July & August counts for four of the most common ones.  With only two years of record for North Bay, it is still too early to determine if these number are high, low, or just normal. 

  • Tunicate numbers seem low in North Bay. Farther south, we are having a very low Tunicate year in LSB which could reflect competition against Corbula clams.  It will be interesting to see how invertebrate trends in different parts of the Bay track against each other going forward.          
  • We are currently in the second year of a huge surge of Corbula clams in LSB: ~35,000 clams in July and ~22,000 in August.  Fortunately, we didn’t see nearly that many in North Bay.  But as always, the perfect number would be ZERO Corbula because Corbula are ecosystem-killing clams.
  • It is also interesting that we find slightly fewer Corbula where we catch Philine. Philine eat young and small bivalves. Coincidence?  The next question is why we find few Philine in the Napa and Petaluma areas.

Tiny Jelly count = 188 in July / 24 in August.  We Identified these tiny Jellies as “Blackfordia virginica” based on their size and the conspicuous X pattern of gut and gonad organs under the bell.  All Jellies in July and August were caught in the Napa River delta.  (We saw a similar surge of tiny jellies in the Petaluma & Sonoma Baylands area in April and May.)

  • Cnidarian jellies, like these, regularly bloom and bust in response to nutrient concentrations and weather.  For some reason, these tiny Jellies bloomed at Napa, in the northeast corner of North Bay, but nowhere else.

We still don’t understand our worms well enough.  Two of our favorites are shown above: The Pile Worm and the “Long Skinny Worm.”  We find both in all parts of the Bay. 

  • The “Long Skinny Worm” seems to be the most widespread and common wherever salinity is above about 20 ppt. It has become a little embarrassing that we still have figured out exactly what species it is.

5. Advanced Parasite Studies. 

Cymothoid Isopod Parasites.  We classify these obnoxious bugs as “Gill Parasites” (Gilpar) in our datasheets.  I still call them “Devil Bugs” in my own summaries.  They are very common around the world in both marine and freshwater ecosystems.  Recreational anglers everywhere are well aware of them.

  • These nasty bugs latch into the gills of pelagic fishes and suck on the oxygenated blood.  In the cooler parts of the year, we occasionally find one or two of them under opercula of Striped Bass, Herring, Anchovies, and even Longfin Smelt. 
  • Cymothoids are highly intelligent!  The tiny bugs have predator-level intelligence.  On instinct alone, they seek their prey.  Each tiny bug knows from birth to insert itself into the gill tissue of an available host. 

Live birth!  Sami pulled this heavily pregnant female Cymothoid crawl out of the gill cavity of a young Striped Bass caught in Gallinas Creek (Station Gal2) in August.  Her belly (brood pouch) was swollen with babies. 

Little babies started erupting just a few minutes later!  We estimated almost a hundred babies.  According to literature, almost all Cymothoid babies are born male.  They turn into females after their first season or two.     

  • Don’t get me wrong.  We don’t like Cymothoids. They are a parasitic burden on many of our favorite fishes. We just admire their intelligence and interesting life history.

Sea Lice.  Caligidae copepods are another type of nasty parasite we occasionally see on sharks, Anchovies, and some other types of fishes. Again, they are common around the world. 

  • The twin tails are egg ducts.  Life is precarious for tiny parasites.  A big part of their survival strategy is to reproduce like crazy to ensure that at least a few young find a host and survive to reproduce again.

If we were to rank our parasites, I would say that Copepod Sea lice are much creepier than Cymothoid isopods.  https://en.wikipedia.org/wiki/Sea_louse 

6. Octopus’s Garden. 

Along the southern shore of San Pablo Bay, offshore from Wildcat & San Pablo Creeks, is the “Seaweed Capital” of San Francisco Bay.  The area is shallow and partially protected from prevailing winds and currents.  Sea ducks, like Surf Scoters and Scaup, and several types of gulls loiter here. 

(I call the Wildcat area “the Octopus’s Garden” because seaweeds are abundant and colorful, and it reminds me of the song of the same name.  In reality, we have never seen an octopus in the Bay, although they are thought to have once been common here perhaps over a century ago.  https://baynature.org/2018/01/30/ask-the-naturalist/octopuses-thrived-san-francisco-bay/ )

  • Non-weed = Hydozoan.  Branching colonies of Hydrozoans are cnidarian animals related to corals or sea jellies. Tiny polyp animals live at the ends of each stalk even though the entire colony looks like a bushy plant.  (For years, I thought these colonies were plants or roots. Then around 2022, Janai Southworth showed us how to examine closely to see their true animal nature.)  https://en.wikipedia.org/wiki/Hydrozoa 

Seaweeds are good food! 

Extracted from Google AI:  For humans – “Seaweed is primarily good for the thyroid gland.  It is an exceptionally rich source of bioavailable iodine and tyrosine which the thyroid needs to produce hormones that regulate metabolism.  Seaweeds are also high in prebiotic fiber and sulfonated polysaccharides that support a healthy gut microbiome.  Antioxidants, potassium, and omega-3 fatty acids in seaweeds help manage blood pressure, reduce inflammation and improve cholesterol levels.”

A word of caution: San Francisco Bay is still slowly recovering from over a century of exposure to pollution from Mercury, PCBs, Chlorinated pesticides and other toxins.  Do not forage for seaweeds in the Bay.  … The Bay will eventually recover.  In the meantime, source your seaweeds from other locations.

Late summer warmth encourages some of the simplest filamentous plant-like organisms to explode.  These slimy “seaweeds tend to take over in shallow-water systems with a relative absence of filter-feeding and surface deposit feeding creatures (worms, amphipods, and clams). 

  • In August, in the shallow embayment offshore from San Pablo Creek (stations Wil6 and Wil7), our net was quickly clogged with masses of green Cladophora.  It had a texture and smell reminiscent of over-cooked spinach.
  • This green-stuff is good food for amphipod-scuds. The only problem here is that there were not enough scuds to control for this warm-season surge.
  • It’s not necessarily a bad thing.  Lots of things eat Cladophora.  Even humans can consume it.  Albeit, Cladophora is a little gross and disgusting compared to the more complex red and green seaweeds. 
  • Cladophora from Wikipidia: https://en.wikipedia.org/wiki/Cladophora 

Farther north, at “Cullinan Ranch,” in the lower end of the Napa system, late-summer warmth stimulated an even simpler lifeform.  These were “chain diatoms;” strings of some of the most basic photosynthetic lifeforms on Earth.  Once again our net was clogged, but this time with brownish, rather than greenish, mush.

  • Diatom mush is good food for tiny organisms. But we don’t yet have enough tiny organisms to exploit this late-summer bloom at Cullinan. 
  • This is primary succession. Unconsumed diatoms will die and rot.  Be patient. With much time, this embayment will fill with sediment, marsh plants will take root, and Cullinan Ranch will become a more robust habitat for fishes and birds.    

Deep thoughts about green and brown muck. Salinity and temperature at Wildcat and Cullinan Ranch locations was roughly equivalent.  Why did we find (A) gobs of green Cladophora at Wildcat and (B) piles of brown diatoms at Cullinan just days apart?  Limited skimming of internet literature gives some suggestions:

  • Green Cladophora is often associated with nutrient enrichment – specifically over-supply of Phosphorus (P) can result in excess Cladophora.  And … lots of birds poop in the San Pablo / Wildcat embayment.  We see flocks of pooping gulls and ducks here most times we visit.
  • Brown chain-diatoms are more dependent on Nitrogen (N). Diatoms, like these, usually signify a relatively nutrient depleted condition.  We occasionally see a few shore birds at Cullinan Ranch, but little else.  And, Cullinan Ranch is not directly tied to creek or river flows.

7. San Francisco Seahawks. 

Ospreys nest in San Francisco Bay in the spring.  The young fledge in mid-summer.  At least that’s the pattern we observed this year.  We see an occasional Osprey passing by, sometimes with a fish in his, or her, talons, in all parts of the Bay.  But, our North Bay trawls take us by two or three well established nesting spots. 

  • Ospreys tend to use some of the bigger starboard side channel beacons in North Bay as nesting boxes.  For at least four months we watched parents delivering fish for the young and then watched young birds start making tentative flights of their own as we motored past.  

When my generation was young, Osprey were amongst the many types of raptors that had become rare primarily due to DDT exposure.  As a result, I still get excited every time I see them. 

Seattle has “the” Seahawks, and I always liked their logo.  Well, SF Bay has Seahawks too.  Deal with it! 

Ringo Starr – Octopus’s Garden (Beatles) (live 2005)  https://www.youtube.com/watch?v=V-BdGchS0yk 

Fieldwork, Fish in Lower South Bay, News
Fieldwork, Fish in Lower South Bay, News