Fish in the Bay – December 2022 – Rain & Brown Water

We trawled in cold and intermittent rain on December 10th and 11th.   This seasonal weather change is a very good thing.  It draws in the winter assemblage of fishes.  Our warm-weather fish friends, like young Leopard Sharks and Bat Rays, migrate to deeper water.  Adult Gobies and Sculpins hunker down in their mating caves.  The winter assemblage of Longfin Smelt, Shad, Herring, and an occasional Sturgeon arrive for either spawning or winter feeding. 


Brown Water!  A big surprise was that the green water we witnessed throughout the last warm season had turned to brown.  Sensors confirmed a strong freshwater lens at most stations. Fresh rainwater tends to float on top over salty Bay water.  Water clarity was a little higher too judging from higher Secchi readings. 

  • All marsh and Bay productivity begins with phytoplankton!  How do we interpret “brown” versus “green” water?
  • Alas, we do not perform phytoplankton analysis. We do not know what variety of phyto this brown water may signify.
  • We must train our eyes to read the water.  We must be ready to identify the next Red Tide bloom. 


Overall fish counts rebounded in December as the winter cohort moved in.  A couple of initial observations:

  • The September thru November increases in Tunicates and Musculista mussels faded away. Respective Musculista and Tunicate counts dropped from 170 & 2,376 in November to 16 & 202 in December.  Could these two organisms serve as a useful surrogate indicator of phytoplankton abundance?
  • Pacific Tomcods have returned. This was another rare oddball fish for LSB until last winter 2021-2022.  We caught another 15 of them this month!


More good news: 

  • Longfin Smelt numbers are increasing! As always, restored Pond A19 appears to be hosting the biggest numbers of spawning Longfins.   
  • Saddleback Gunnel. This is a new fish for LSB! – Discussed further below.
  • A White Sturgeon was caught at Art3 and three more were spotted on sonar at Coy1.


1. Cold & Rainy Days on the Water.

The hills to the east were dusted with snow.  It was a solid indication that the cold season had arrived.


The “San Jose Bowl” loomed to the south of us as we arrived at the Alviso Marina on Sunday.

The San Jose Bowl.  I still don’t know if this is a figment of my imagination.  It always seems to be a little less rainy in the vicinity of the City of San Jose and the Alviso Marina.  The Sun intermittently peaks through otherwise solidly overcast winter skies over the city itself.  Is this real?

I first wrote about this “atmospheric bowl” two Decembers ago in this blog: 

  • As explained there, many years earlier Joanna De Sa, then the Chief Plant Operator at the San Jose-Santa Clara Regional Wastewater Facility, told us that rain seems to avoid the City of San Jose and much of Silicon Valley. Wastewater treatment plant operators are always cognizant of the rain.  Rain leads to increased sewer flows and potential flooding.  Yet, somehow, the SJ-SC RWF service area never seemed to experience the full brunt of precipitation that was measured in adjacent areas all around it.   
  • I imagine cold Pacific winds hitting the outer coastal mountains, dropping some precipitation, then lofting upward and eastward over a warm urban heat island. But, I could just be rationalizing from shapes in the clouds.
  • Having said all that, and for the record: rainfall was fairly plentiful over Alviso Marsh this weekend. Rain and cloudy skies impeded our photographic fish examinations on both days. 


2. Longfins & the Winter Fish Assemblage.

Longfin Smelt.  Longfins continue to arrive for the 2022/23 spawning season.  The monthly count jumped from 79 in November to 498 in December.  Luca alerted us that the Longfins in Pond A19 alone set a new record Longfin count for a December.  Hopefully, this winter’s Longfin increase will continue, but the season is still early.  


Three winter fishes!  Top to bottom: American Shad, Longfin Smelt, and Pacific Herring.  Photo by Luca

Winter fishes.  In addition to 498 Longfin Smelt, 39 American Shad and 2 Pacific Herring were netted.   All three species return upstream each year for spawning or recruitment.  However, unlike Longfins, neither Shad nor Herring are regular spawners in these marshes.   


Two English Sole, two Ctenophores, and other critters at LSB2

English Sole.  Ten English Sole were caught in December.  Larval to very young English Sole also swim into the Bay each winter.  They sniff out cool fresher water from off the coast then chase it upstream into lower-to-mid delta mouths of creeks and rivers.  We should see many more young Sole over the next few months.

Ctenophores, aka Comb Jellies!  The crystal clear orbs shown just below the two English Sole are Comb Jellies.  We caught 50 of them this month.  That is still a low number by comb jelly standards, but we have seen ZERO since June 2021.

  • Comb Jellies always seem to be on a boom or bust cycle. Their populations explode when copepods and other near-microscopic zooplankton are abundant during the cool side of the year – roughly November thru June. Abundant literature tells us that Comb Jellies exert major control over zooplankton populations. 
  • Think of Comb Jellies as a ‘clean-up crew,’ or ‘natural circuit-breaker.’ Without Comb Jellies, zooplankton populations would grow unchecked until they consumed all phytoplankton.   



More Winter Fishes.  Each fish has a story, but sometimes it takes a while to figure out the story.

Sanddabs.  We identified 46 Speckled Sanddabs and 33 Pacific Sanddabs. We catch both types here.  This was a very good December catch.  Sanddab numbers usually peak around February.  

Staghorn Sculpin.  8 Staghorns were counted. Adult Staghorns also arrive with the cool weather.  Males establish spawning caves or hollows.  Females swell with eggs and eventually seek an attractive male and burrow to deposit them.  (The Staghorn shown above appeared to have a belly full of eggs.)  

Pacific Herring.  As mentioned above, Herring also arrive for winter spawning.  However, the two individuals caught in December were very young and likely only a year old at most.  Herring usually spawn farther north in SF Bay.  

Pacific Tomcod.  15 Tomcod were caught in December.  This is still a bit odd.  We saw 13 Tomcods in January through May 2022.  Prior to that, only one or two were ever seen here.  Tomcods are the smallest of the Cod/Pollock/Hake family of highly edible near-bottom feeding fishes on the Pacific Coast.  Whether this Tomcod arrival in Lower South Bay is normal or beneficial is still a bit unknown.    


More examples of winter fishes caught at Coy4.  The Bay Pipefish is a year-round resident.


3. Interesting Small Critters

Northern Anchovies!  At least a third of the 215 Anchovies caught in December were very young juveniles at LSB stations.  This is another strong sign that last summer’s spawn was a success!  These youngsters will likely mature farther out in the Bay and return for next summer’s spawn.  2022 stands as our record Anchovy year by far: 13,621 were caught.  No other year comes close! 

Nudibranchs!  We counted 25 Enosima aeolid nudibranchs. This is a new record.  Prior to 2021 we only ever saw one or two of them over several years.  Is this a new invasion?  Or, is this merely the latest resurgence over many years?  What are these attractive sea slugs eating?  Why are they here now? 

Crangon Shrimp.  We caught 958 Crangon in December.  That is the highest number we have seen since May or June.  The 2022 Crangon total was just over 16,000.  Prior to 2018, that would have seemed a good number, but all yearly totals since then have been much better.  Given that context, 2022 was a disappointing Crangon year. 

  • Crangon, particularly Crangon franciscorum (the “brown-tail” species) rely on good rainwater flushing to support the recruitment of their young. These salty drought years simply do not support them well. 
  • Interestingly, we saw many of the more saltwater/marine adapted Crangon types in the catch: “Blue-spots” (C. nigromaculata), and “Black-tails” (C. nigricauda).  


4. River Monsters & a New Fish.

White Sturgeon (1.6 meters/5 feet 3 inches long – total length), Art3, 10 Dec.  Photo by Luca.

White Sturgeon. One Sturgeon was caught at station Art3 on Saturday.  Luca described it as “impressively large.” Three more Sturgeon were observed on sonar just a little farther downstream at station Coy1. 


Micah passes the big Halibut to Luca to release at Coy4.

California Halibut.  This was the only Halibut caught in December.  The year-to-date Halibut total is 48.  We catch a big Halibut once or twice each winter.  This one was one of the biggest Halibuts we have caught in LSB.    

  • Literature says that Halibut populations increase during El Ninos, and our own LSB data support that. 2015 stands as our record Halibut year in LSB, by far.  Halibut were much less abundant over last several years after 2016.
  • Halibut are members of the “Large tooth” flounder family. If you ever catch one, be sure to keep your fingers away from those big teeth! 


Saddleback Gunnel at Coy1, 10 Dec 2022.  Photo by Alec Scott.

Saddleback Gunnel (Pholis ornate).  NEW FISH!  This was the first Gunnel we ever caught in Lower South SF Bay.  Their elongated eel-like bodies enable them to hide in seagrass beds and in crevices. 


5. All’s well that ends well.  

Heading home at the end of December trawls:  Micah at the helm.  Alec stowing gear at right.  Luca giving two thumbs up for another great trawling weekend.

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