Fish in the Bay – December 2020: The Longfin Chronicles, part 1.

Longfin trawl results from December 20th.

Operation “Save Our Smelt” 2020/21 has begun.  This is the third year that researchers have been conducting additional trawls to collect large adult Longfin Smelt.  Their goal is to establish a sustainable breeding colony in tanks at the “Fish Conservation & Culture Laboratory” (FCCL) near Byron, California.

I originally described this project a couple of years ago in this blog post:


1. The Hard Part: Collecting Longfins for Broodstock.

Zero-dark-thirty at the Alviso dock.

Micah Bisson, Rachel Fichman, and I embarked early on December 20th for a morning of three-minute trawls at 10 locations along Lower Coyote Creek shown in the map above.  


The collection tank.

As in previous years, an insulated collection tank is filled with Bay water from the Longfins spawning area.  Only around 20 Longfins are collected per day to minimize crowding.  When we are close to filling our quota of 20 big “keeper” fish, the FCCL staff is notified to meet us at Alviso dock for precious cargo pick-up as soon as we pull in. 


Micah and Rachel trawling as the sun rises over Lower Coyote Creek.


Rachel empties the trawl net into the sorting tub.

Short-duration 3-minute trawls are performed to minimize fish stress.  Any injury or trauma to the fish could jeopardize this project and the future of these threatened fish.  


  1. Micah carefully separates any Longfins from other fish and bugs using a dip net.
  2. Longfins are then floated into a collection cup.
  3. Any Longfins less than about 80mm long in standard length are quickly released back to marsh waters. Hopefully, even these small rejects will also live to spawn another day.


A big fecund Longfin Smelt is released into the collection tank.

Big Longfins (the “keepers”) are transferred to the collection tank. This tank is aerated and cooled with ice bags to keep water quality at ideal Longfin spawning parameters.  Oxygen is pumped up to 100 percent saturation.  Cooling keeps temperature at or near the single digits in centigrade.  These parameters are maintained at all times, from capture in the Bay until delivery to the FCCL lab in Byron. 


2. The Easy Part: Other Fish & Bugs.

While Micah and Rachel cared for Longfins, I examined other critters from the net.

Winter Run Anchovies? – Four Anchovies: three dark blue-backs plus one very faded blue-back.

Northern Anchovies.  Something strange is happening with our Anchovies, and we have seen this in recent years past as well. 

Summertime spawning Anchovies practically disappeared after the early November cold-snap.  Since then, there has been a slight rebound in numbers. But, many of these winter Anchovies are long, dark, and very blue.  At least some of these are recent arrivals from the deep-blue sea.   I suspect this is a separate population from our summertime spawners. 

(The one drab-gray faded fish in photos above may have arrived weeks earlier?  Or perhaps it is a straggler from the summer-time population?) 


Long, sleek, blue-hounds of the sea – especially the bottom one!

Anchovy dorsal color fades away within days to weeks as they linger in the Bay, particularly during the warm months.  These larger dark blues look like new arrivals that were drawn in from the ocean by the cold temperatures. 

Are the Anchovies shown above a different breed: a cold-water, marine variety?  Comments from any Anchovy experts are most welcome!


Juvenile Anchovies with blue crowns.

However, the LSB Anchovy picture is complicated:  small recruits from last summer’s spawn still comprise most of the Anchovies caught.   

  1. These babies are the new generation. The summertime Anchovy spawn was successful!
  2. The youngsters also show flashes of blue. All LSB Anchovies turn bluer when salinity is high, and the absence of winter-time rain thus far has kept LSB saltier than usual.  — Nonetheless, the blue babies are not as large, not as dark, nor as brightly colored as the adult new arrivals.


Larger young-of-year Anchovy showing traces of blue, but no darkness.

Even the older Anchovies that grow up in the Bay do not darken like those from the ocean.  The Bay-resident Anchovies develop a small amount of blue or green color in the crowns of their heads and along the lateral line, but full dark and vivid color seems to require some time at sea. 

And, what’s up with this blueness?  As mentioned in previous blog posts, biologist Carl Hubbs described San Francisco Bay Anchovy colors he, and local fishermen, saw in 1925: clear, pinkish-brown Anchovies lived in the Bay; green-backed Anchovies swam in from the ocean. Blue was never seen back then.

Anchovies are blue now.  … To be continued.


American Shad from Mud Slough.

Salinity at all stations ranged from the mid-to-high teens in parts per thousand (ppt) on the 20thHence, the several American Shad that were caught were all green to bronze-brown on their dorsal sides. 

Like Anchovies, Shad turn blue in higher salinity (around 19 ppt and above).  When exposed to brackish or fresher water Shad change to green then finally deep-chocolate-brown as salinity drops to the single digits.  (See

LSB is still too salty!  Longfin Smelt young need fresher water, below 10 ppt, for successful recruitment.  We need salinity to drop to “Brown Shad levels.”  Pray for rain!


Young Shokihaze Gobies from Lower Coyote Creek.

Shokihaze Gobies.  We are seeing a lot of these babies this year.  This appears to be a population explosion to some extent.  Shokihazes seem to like the saltier water.  They are cute, non-native, and here they are!   


Shiner Surfperch – A faint golden “W” is emblazoned on its side.

Shiner Surf Perch.  These shiny fish are not as common here as they were a few decades ago.  But, they continue to show up here and there.  Overall, Shiners are still very common along the coast.


2-inch Diamond Turbot.  These can grow up to 12 to 18 inches closer to the ocean.

Diamond Turbot.  We net these native marine flatfish once or twice per year, always as small juveniles, roughly 3 inches or less.   They are a common type of flounder in bays in Southern California, just a little less common here.


This is Sturgeon season.

White Sturgeon.  The fish-finder sonar spotted this one 14 feet below the boat.  They cruise along the bottom looking for slippery food, like lampreys, to suck up with their vacuum cleaner mouths.  They eat small fish, clams, shrimp, or any other tasty critters.


Crangon franciscorum.  Crangon shrimp numbers are alarmingly low this winter!  Two years ago, our 5-minute trawls typically netted 1,000+ Crangon.  This year, 3-minute trawls are catching 10 to 15 shrimp at most!  We heard from the Laine’s Bait Shop people that they are seeing very few Crangon this season as well.


Crangon female with a yellow egg-mass growing just behind her head.

This is the Crangon brooding season.  We should be seeing thousands of big females with clutches of eggs.  Instead, we see a few with growing egg-masses and only one or two fully-berried females so far this year.

I hope this Crangon situation turns around soon.


3. FCCL Picks up Precious Longfin Cargo.

Alejandro & Anna with the Longfin Collection tank at Alviso dock.

FCCL team members, Alejandro Ruiz and Anna Neill, picked up our collection tank with 20 keeper fish – 4 males, the rest were females. 


Rachel completes custody sheets as Alejandro and Anna secure the tank for the one-hour drive back to the FCCL lab.

The overall target is to collect 200 Longfin Smelt for the FCCL broodstock this season.   So far each trawling expedition has caught its quota of 20 big adult keepers.  We found Longfins at every station we trawled.


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