Fish in the Bay – Marine Heatwave Watch – May 2026.

May 2, 2026 Jim Ervin
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Fieldwork, Fish in Lower South Bay, News

This is a small summary of our May trawling results in San Francisco Bay:  4 sites in San Pablo Bay to the north, 2 sites in South Bay, and 2 in Lower South Bay (LSB) in the far south. 

We are entering a particularly special time-period for our fish and bug surveys. A strong marine heatwave is spreading across much of the North Pacific and the coast of California.  Plus, NOAA predicts a good likelihood that conditions at the equatorial Pacific will shift from neutral to El Nino sometime this fall.

  • Weatherwest – Special update: Rising odds of a strong-to-historic El Niño event in 2026, with growing likelihood of significant regional-to-global scale impacts https://weatherwest.com/archives/43880 
    “El Niño also acts as a “thermostat” for global climate by liberating years’ worth of accumulated heat stored in the subsurface tropical Pacific Ocean and dumping it into the atmosphere, where it eventually dissipates–but not before warming the entire planet in the meantime. Thus, El Niño raises global average temperatures temporarily acting, essentially, as a 6-12 month long “mini global warming” event.”
  • “Godzilla” El Niño May Have Begun, Here’s What This Means for Earth
  • I am not suggesting an impending disaster.  Fishes and bugs in SF Bay have survived many severe human-created catastrophes over the last 150 years: Hydraulic mining waste, marsh destruction, oyster farming, salt production, and freshwater sequestration quickly come to mind.  But additional heat will stress them.  Already, Halibut are numerous, and pelagic fishes are relatively scarce.  We must be on watch.  A repeat of the July/August 2022 fish-killing red tide would be at least a moderate-sized disaster.

The table above summarizes fish and bug totals at all eight monitoring locations in the Bay. 

  • Overall fish totals continue to be low and very disappointing.  Our most numerous pelagic fishes like Anchovies, Herring, and Shad, prefer cooler water, and hence are less abundant. 
  • Warmer-water fishes, Halibut, Tonguefish, and possibly Drums and Croakers (?) are more numerous than average.  

I was not present for the May trawls due to family circumstances.  However, Sami diligently photographed trawl results for May. Partly for that reason, this photo summary and the data analysis features only Lower South Bay (LSB) with particular emphasis on water colors at each station.

  • The other six stations farther north in SF Bay are still of great interest, but we only have a bit over a year of comparable data.  It’s not yet possible to compare fish and bug populations against more than a decade of history.
  • We are re-training our eyes to be on the lookout for red tide blooms as this 2026 warm season develops!

1. Artesian Slough Experience in May.

The typical LSB 2-day trawl effort starts in Artesian Slough where the SJ-SC Regional Wastewater Facility discharges to Coyote Creek and on to the Bay.  I have discussed this experience many times in previous reports. It never gets old for me. 

  • Clear water looked almost black in May, like peering into a deep lake or well.  In technical terms, Sami recorded the darkish color as somewhere between Courtyard (#30) and Hunt Club (#31) on our Kudela Lab/Sherwin-Williams color scale.
  • This dark, clear water ‘browned down’ quickly by the next station downstream.  Microscopic planktonic life explodes as Bay water mixes with the fresh.  Single-celled plants (or plant-like animals) multiply into billions, making the water murky.
  • Just a few hundred feet farther downstream, a “surface scum” appeared.  Much of this was dead phytoplankton that expired from salinity shock at the junction of Bay and fresh waters.

Water continued to shift progressively browner farther downstream.  Massive amounts of sloshing suspended sediments accounted for most of the brownness, but vast populations of brownish floating diatoms also added to the look. 

  • Diatoms and other phytoplankton are food for larger organisms.  Not surprisingly, phyto abundance is rapidly exploited by many varieties of filter-feeding and surface-deposit-feeding tiny bugs. 

Amphipod count = 1,841 – Artesian Slough accounted for 1,630 of this total! 

  • Amphipods are tiny crustaceans that are roughly analogous to ants, termites, or bees in the terrestrial ecosystem.  They are efficient detritivores, occasional filter-feeders, and excellent food for fishes and birds. Based on Amphipods alone, the waters of Artesian Slough appeared not just healthy, but super-abundant – as is usual.    

Artesian Slough empties into Coyote Creek.  Biomass in Coyote Creek transitions increasingly into bigger bugs, like shrimp, or to fishes.

Yellowfin Goby count = 85 / year-to-date = 371.  This is a low year for Yellowfins, but there have been lower years.  Gobies are not much affected by the ENSO cycle.  Yellowfin ups and downs are probably more affected by competition with other gobiids here.

Corbula Clam count = 4,380 / year-to-date = 25,849.  Good news: Corbula numbers are down by half.  Last year at this time, we counted over 53,000.   Bad news: This is still the highest Corbula count we have seen on record, aside from last year – by far. 

El Nino-like warmth across much of the north Pacific in 2026 seems to be boosting numbers of Halibut and sharply reducing populations of Sculpin, English Sole, Anchovy, and Shad.   

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. 

Staghorn Sculpin count = 61 / year-to-date = 129.  The Sculpin count for May was not too bad, but the 2026 year-to-date Sculpin count is our lowest on record.  Only last year, and the 2015 and 2016 years, were nearly so low.  

2. Upper Coyote Creek & side sloughs.

As the UC Davis team boated farther out into upstream marshes, water color settled out into a fairly consistent shade of “Mélange Green.” 

The greenish/brownish hue is influenced by season, stage of the tide cycle (ebb, flood, or slack), and, believe it or not, by phase of the Moon (neap or spring tides). 

  • Fast moving water during ebb and flood tides kicks up sediment.  That makes the water visibly browner/yellower. 
  • During spring tides brownness/yellowness persists in this shallow part of the bay through almost all of the tide cycle.  For a long time, we noticed that water was consistently browner when the Moon was full or new.  We thought it must be the magical power of the Moon Goddess.  Eventually, we realized it’s gravity.  (To be fair, gravity is a magical power.)
  • The normal shades of water color are not particularly important.  It is only important that we keep our eyes trained for any possible fish-killing red tide.  Red-brown, orange, or dark brown water would be cause for alarm and additional sampling.

Longjaw Mudsucker count = 2 / year-to-date = 29.  Mudsuckers are a very special native gobiid.  They are sentinels of healthy pickleweed marsh. The current count of 29 for the year-to-date is very good – maybe a little higher than average.     

Arrow goby count = 9 / year-to-date = 54.  Arrows are the tiny (~1.5 inch long) snake-like natives that mainly live in warm, muddy shallow waters.  This year’s count is fairly normal.

Dr Hobbs usually schedules trawls to be at the shallowest sites, like Pond A19, near slack high tide. (Slack tide = greener water.)  By the time the team reached station UCoy2 close to 2 PM on the day of trawling, sediment from fast-moving ebb tide ‘browned-down’ water color to “Antiquity” #25 on the Sherwin-Williams color scale.

Marsh wren nests: Wren nests were spotted in nearly every stand of tall California bulrush along the sides of sloughs. These little brown birds move fast and are hard to spot, but their nests and springtime twittering calls are impossible to miss.    

Shimofuri Goby count = 2 / year-to-date = 129.  Shimos numbers exploded in the later part of 2020.  Then, their numbers dropped considerably after 2023.  Much of this fluctuation seems to be competition with Shokihaze gobies. We suspect that warmer, saltier water tends to favor Shokihazes at the expense of Shimos. 

3. Alviso Slough.

The second day of May trawls started in Alviso Slough – the mouth of Guadalupe River.  Similar to Artesian Slough, fresher river water in early morning appeared greener and less turbid (Mélange Green on the color scale). The upstream Alv1 station supported more bottom dwelling bugs. 

Corbula clams were much less abundant in Alviso Slough compared to Coyote Creek farther upstream.  There were many dead shells at Alviso.  And almost all surviving clams had barnacles growing on them. 

  • As mentioned in previous reports, barnacles and other sessile marine organisms like tunicates, anemones, and hydrozoans seek hard substrate for footing.  Lower South Bay substrate is almost entirely soft mud, hence surface-dwelling Corbula clams are prime anchoring spots. Sessile organisms don’t seem to harm clams directly, but a bulky animal attached to the shell probably affects clam mobility in ways more bad than good.  Plus, we see many instances where an attached barnacle has glued the clam’s valves shut – that can’t be good.
  • Even more interestingly, we are finding many more barnacle-infested clams at upstream station Alv1 in 2026 compared to 2025.  The explosion of Corbula clams itself may have helped barnacles proliferate by providing hard substrate.  This in turn may serve as a control on Corbula populations (a negative feedback). 
  • This biological negative feedback loop seemingly complies with ‘Le Chatelier’s principle’ (developed from chemistry and thermodynamics): “… if a dynamic equilibrium is disturbed by changing the conditions, the system will shift its position to counteract that change and re-establish equilibrium.”  https://en.wikipedia.org/wiki/Le_Chatelier%27s_principle
  • Is this cutting-edge clam science, or what!?!

At the end of Alviso Slough water became more turbid and color shifted at least one degree browner (from “Mélange Green” #26 to “Antiquity” #25).  This station (Alv3) is at the confluence of Guadalupe River with Coyote Creek as they empty into Lower South Bay. 

Again, as we saw in Artesian Slough the previous day, a surface scum of dead phytoplankton was conspicuous where fresh and salt waters ultimately collide. (Salinity at Alv1 & Alv2 stations upstream was around 6.5 ppt.  Salinity at Alv3 was 11.3.)  Dead phytos and lots of other nutritious detrital stuff piles up here.  Shrimp and bigger fishes move in for the feast. 

Striped Bass count = 3 / year-to-date = 10.  At this point, this is our lowest Striped Bass year on record.  Striped Bass and all other pelagic fish counts are very low in 2026.  Dr. Hobbs suspects current warm temperatures are either pushing Striped Bass out into cooler coastal waters or perhaps suppressing their populations altogether.   But, who knows?

4. Coy4 & LSB.

Station Coy4 is the ultimate end of the Coyote Creek & Guadalupe River systems.  From here they empty into Lower South Bay. 

This place is usually a “shrimp hotspot,” but not so much this day:  The 394 total shrimp was low by historical standards.  Shrimp were split 50:50 between non-native Palaemon and native Crangon.  Shrimp populations in 2026 are close to 1/10th the 2018-to-2015 average. Is this a consequence of the Corbula clam explosion!?!

In other news:

Bay Goby count = 19 / year-to-date = 27.  Native Bay Gobies have become quite scarce in LSB over recent years. But surprisingly, the 2026 YTD count is well above average for the last decade.  Does warmer water or higher salinity favor Bay Gobies over the several non-native invaders? 

California Tonguefish count = 44 / year-to-date = 59.  These California natives are the consummate “El Nino” fish.  This is the most Tonguefish we have seen in a single month since June 2015 – at the middle of a huge El Nino with the warm water “blob” in the North Pacific.      

Bat Rays showed up far downstream, in the middle of LSB in May.  That’s also where we found most of the tiny Cheekspot gobies.

Bat Ray count = 12 / year-to-date = 20.  All Rays were young-of-year, probably born in the late warm days of 2025.  Rays and sharks avoid fresher waters as much as they can. They tend to scatter far downstream during the wet months of winter.    

Cheekspot Goby count = 36 / year-to-date = 58.  Cheekspots and Arrows are our two tiny native gobies.  In some parts of the Bay, they live nearly side-by-side and can be very difficult to distinguish from each other. 

  • In general, slightly more snake-like Arrows prefer soft and muddy substrate and warmer, shallower waters.  Cheekspots tend to reside on harder substrates and in deeper, cooler water. 

5. Coyote Creek 2/3 & Pond A21.

The flushing force of ebbing spring tide caused all LSB waters downstream of Alviso Slough to ‘brown-down’ to a warm shade of “Antiquity” (#25) in the early afternoon of May 1st.   

Shokihaze Goby count = 7 / year-to-date count = 246.  Shokihazes and Shimofuris are the two non-native mid-sized gobies from Japan.  Shokis prefer slightly saltier water. Shimos tend to be more comfortable in fresher water.  But the two overlap and compete.  

  • So far, 2026 is a very good Shokihaze year – and a relatively bad year for Shimofuris. 

The UC Davis crew ended the second trawling day in May in restored Pond A21.  Eight Anchovies, a single White Croaker and some other assorted fishes were netted here. 

Anchovy count = 57 / year-to-date = 718.  Anchovy numbers are usually pretty low in LSB from January through May.  Adults return for spawning during the warm months.  So far, this year’s numbers are on the low side, but not the lowest.     

White Croaker count = 1 / year-to-date = 11.  As hard as it is to believe, 11 Croakers is our record count in LSB for any year since at least 2012 – and it is still only May! 

  • One shouldn’t make firm conclusions from such a small sample size.  But, I will anyway. … Some published studies of the Croaker & Drum family of fishes report that they recruit best in warmer waters.  (In Southern California, White Croakers are nicknamed “Sewer Trout” because they tend to be numerous near warm, nutrient-rich effluent streams from wastewater treatment plants.)  
  • Are these 11 young Croakers of 2026 yet another indication of warmth in LSB and California coastal waters???  If we don’t know, who does?

Arrow – Hot Hot Hot [Official Lyric Video]  https://www.youtube.com/watch?v=5HDgGzI0Pb8

Fieldwork, Fish in Lower South Bay, News