Fish in the Bay – March 2024, Spring Flush Continues.

As of March, we were still experiencing a welcome extended rainy spring.  In theory, the additional rainwater flushing should be very good for finfish recruitment in Lower South Bay (LSB) and that still may turn out to be true. 

However, overall fish counts were a bit low.  – not historically low; just lowish.  Perhaps the past two blockbuster years have unreasonably raised our baseline expectations?  Or, perhaps we just need another few months of data to put this slight fish lull into perspective. 

Good news #1: Marsh restoration continues.
OpenRoad: Largest wetland restoration project on the west coast (Episode 91)


Good News #2:  Starry Flounder numbers remain unusually high.  The YTD count is over 200 at this point. 


Good News #3:  California Halibut babies are still surging with this year’s El Nino.


1. Charismatic Fishes.

Longfin Smelt count: 64.  Good News!  Both this month’s Longfin count and the year-to-date count (1,170) would be record catches in any year prior to 2022. 

Bad News: Longfin spawning season ended abruptly.
 On March 10th, only two Longfins were caught from all upstream stations.  Longfins had vacated all spawning grounds!  Salinity was still low. But it seems that water temperatures above 15 degrees C may have signaled the Longfins to retreat to cooler and deeper water.

  • Alas, we irrationally hoped that Longfins would continue to spawn for at least a few more weeks.      


Sturgeon on Sonar.  Two shadows were spotted at Coy1, but only one was positively identified as a Sturgeon. 


Sami and Niko lift the big fish at UCoy2, 10 March 2024.

White Sturgeon.  We were very excited to catch this big girl Sturgeon.  (At least we think she was a girl.)  She was rather chubby – possibly gravid???  She measured 1.5 meters (59 inches) and weighed at least 100 pounds.   

With great fish comes great responsibility. 
We see Sturgeon on sonar quite frequently during the cool season, but catches are rare, and frankly, not entirely desirable.  These big fish don’t need the stress.  Their size, weight, and sharp scutes pose some risk of injury to both fish and human handlers.  Fortunately, Sami and Niko had the needed strength and agility to lift her aboard, take her out of the net, and return her back to the water safely within two minutes. 


Rare Oddballs:

White Seabass. This is the fifth White Seabass caught in Lower South Bay since monitoring began in 2010.  Seabass #4 was caught during Broodstock trawls a week earlier on February 28th. Interestingly, these two normally marine fish were both caught at locations where salinity was only between 12 to 16 ppt. 

Contrary to their misleading name, White Seabass are members of the Croaker family.  They are a popular coastal game fish.  Anglers fish for them near the Golden Gate. Sami suggested that these stray juveniles probably wash in from the Golden Gate population.


White Croaker (aka “Kingfish” “Sewer Trout,” “Butter Bass,” etc.”).  This is the first White Croaker we have seen since May 2021.  He (or she) was newly hatched, about one centimeter long, and missing most of the tail. Croakers were supposedly common in LSB once upon a time.  Now, they are extremely rare. … Is loss of the “Sewer Trout” actually a good sign?   


Bay Goby.  Like the White Croaker, the Bay Goby is another “missing fish.”  They used to be THE native mid-sized Goby in LSB.  Since 2010, we never see more than a few dozen babies in any given year.  They have been completely displaced by non-native Yellowfin, Shimofuri, Shokihaze, and Chameleon Gobies. 


Striped Bass count = 11.  All Striped Bass caught in March were tiny babies.


Bay Pipefish count = 17.  All Pipefish were caught at downstream stations.  They appear to be avoiding low salinity at upstream stations.


Shimofuri Goby count = 75.  The March Shimo count is still low, but it will almost certainly increase later in the summer.   Shimos surpassed Yellowfin Gobies as our most numerous gobies in 2021 and 2023.  More likely than not, they will do it again this year.

Shimofuri Identification.  The two specimens shown above are mature adults. Their colors intensify with the approach of the March through September spawning season – if the water is relatively fresh. Water salinity in these two instances was 1.7 and 3.2 ppt at stations Art3 and Dmp2 respectively.

  • Identification tip #1: Many small spots cover the cheeks and extend under the jaw-line. The name, “Shimofuri,” means “Frost Covered” in Japanese.
    To put it another way, Shimos have frosted faces.
  • Identification tip #2: Orange margins on both anal and second dorsal fins. The orange margins are almost always conspicuous when salinity is low, but sometimes fades away completely in higher salinities, roughly at or above 18 ppt.


Chameleon Goby count = 32.  Chameleon Gobies are close cousins of Shimofuris that live in saltier water.  They are such close cousins that the two species were considered one for many years until Akihito and Sakamoto (1989) first provided detailed descriptions.,Matern%201999%3B%20Wang%202011).

  • Identification tip #1: Red band on anal and second dorsal fins. (The red band is more conspicuous on the anal fin.) The Japanese name for Chameleon Goby is “Akaobi” which literally means “Red Band.” 
  • Identification tip #2: No spots under the jaw and fewer and larger spots on the cheeks.
  • Identification tip #3: White margin and black band on the anal fin. This black and white contrast on the anal fin is sometimes the most conspicuous feature when the fish is tiny, wet, and wriggling.
  • Advanced Identification tip: Body shape and eye interorbital distance.  Shimos are more torpedo shaped and have slightly arched backs.  Chameleon Gobies have boxy faces and straighter bodies. The scientific descriptions of these features are more analytical and exacting. 

Note of acknowledgement:  I learned the above identification tips and the Japanese names of these fish via email from Mr. Munenori Kishida last November. He is the chief of scientific research in support of Emperor Emeritus Akihito at the Biological Laboratory of Imperial Palace (BLIP) of Japan.   


2. Flatfishes.

Starry Flounder count = 53.  The Starry population boom that started last May continues.  Starries have gotten progressively bigger each month over the past year, from tiny babies the size of a button to almost frying pan-sized now.  The real test of ongoing success is coming soon.  


Three Baby Halibut (left) and four young English Sole (right), LSB2, 9 March 2024.

California Halibut count = 31.  Baby Halibut continue to arrive with the El Nino spring.  Though far short of a record, this is the highest March count we have seen in several years.

English Sole count =  17. The Sole count remains moderately low as is expected for this La Nina fish. As usual, many of these young Sole display gruesome-looking protozoan X-Cell disease tumors


3. Shrimp Wars.

Crangon count = 841.  Native Crangon numbers are only moderate so far.  We continue to see brooding females at stations Alv3, Coy2, and in Pond A21.  Tiny baby Crangon are starting to show up at upstream stations.

Palaemon count = 1023.  Similarly, the Palaemon shrimp population is off to a strong start.  Many Palaemon are already gravid as the season warms.

Exopalaemon count = 285.  Exopalaemon are still relatively scarce.  As usual, the vast majority were caught in Dump Slough.   

Mysids. The springtime Mysid bloom continues to look very robust this year.  – All we need now are more fishes to eat them! 


4. Strange Invertebrates.

Mossy Bryozoan (top) & a tray full of Corbula clams (bottom) at Alv1

Corbula count = 1,664.  Bad News!  This was a significant Corbula blowout for so early in the season.  Over 85% of the clams were collected at station Alv1 alone.  The upstream end of Alviso Slough supports a very dense assemblage of these non-native mollusks. 

Mossy Bryozoan.  As always, the biggest and fluffiest balls of Mossy Bryozoan (“Bryo-balls”) were also found at Alv1. 

  • Abundant filter-feeders like these at Alv1 point to availability of microscopic food flowing down from the Guadalupe River.  


Musculista count = 61.  The number seems low, but it is a March record.  We have only observed Musculista (Asian Date Mussels) sporadically since 2016, then with alarming frequency starting in mid-2020. 

  • Musculista numbers skyrocketed from July to December 2022 and then again from August to December 2023.

As of March 2024, the Musculista number is still relatively low, but we collected large gobs of muddy shell-encrusted byssal mats at both LSB stations.  This is a major change from rock-like encrusting bryozoan “bryoliths” and ancient oyster shell hash we used to see here.  The geographic extent of this new ecosystem landscape is unknown at this point.  The effect on habitat for small bottom-dwelling organisms is likely profound.


Philine “Bubble Snail” count = 48.  This is the most Philine we have seen since December 2022. They were more abundant during the drier years of 2018 and 2020 thru 2022. We are still experiencing a wet winter/spring, so this apparent resurgence should be short lived. 

Hydrozoans.  We continuously pick up scraps and fragments of different types of Thecate Hydrozoan colonies.  These almost-microscopic animals (zooids) are members of the cnidarian phylum along with anemones, corals, and jellies.  The colonies look like plants, or plant roots. For years I failed to recognize them until Janai demonstrated their true identity.

  • Each branch of the root-like structure contains dozens of individual polyps. Most serve as filter feeders, others specialize as reproductive units or stinging defenders.  Altogether, these bushy colonial masses provide essential carbon-cycling and refugia services.
  • I don’t yet know the exact varieties we have here. From physical appearances, there seem to be at least three general types of hydrozoans in Lower South Bay sloughs:
    1) A “root-like” hydrozoan in lower salinities.  This one is softer and darker brown. 
    2) A “branching” hydrozoan at mid-salinities.  It is more orange in color and individual polyps are more conspicuous.  (I think this one might be called “Obelia.” But that is just a guess.)   
    3) A “bristly” hydrozoan in deeper waters with higher salinities. These colonies appear stiff and come in lighter shades of yellowish to tan.   
  • Not surprisingly, all three hydrozoa types are more conspicuous from spring through summer. They die back a bit in colder weather – probably mirroring trends in phytoplankton abundance, salinity, and temperature.
  • Wikipedia – Leptothecata:


Sun Halo at Alv3 on 9 March 2024.

Scary thought:  As we examined fish and bugs at Alv3, a ‘Giant Eyeball In The Sky’ examined us.  This kept us on our best behavior.


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