Fish in the Bay – December 2019: Part 1, Rains bring Mysids and other critters.

December trawls: Jon Kuntz was on lines and net duty.

 Happy New Year!  I am catching up on December reporting.  As you may recall, a first special installment focused on colorful American Shad.  This report covers some of the other bugs and fish.


Trawl map.


Bay-side station trawling results.


Upstream of Railroad Bridge.

More fish with rain!  As mentioned in the previous colorful Shad special report, our December fish count at 20 stations increased from 148 in dry early-November to 432 from bomb cyclones & an atmospheric river on the 7-8 December weekend.  Rain was showering the hills as we trawled.


Allen Huyen, a bug expert, handled water quality instruments and winches.


1. Critters on the move following the late 2019 freshwater flush.

Mysids at Art2

Mysids were blooming almost as soon as the rain started to fall.  This is a very good sign.  Blooming mysids are forage food for everything bigger than them. Essentially this place feeds itself as long as mysid and copepod growth keeps up.

Note to new readers:  Mysids are essentially “midget shrimp.”  They are NOT true shrimp, but they are related crustaceans.  Mysids are a key link in the food web.  They are delicious.  Practically every creature in the marine and estuarine world larger than a pinky finger eats them.  Most of the fish and birds we care about in this ecosystem depend on massive blooms of mysids.


Rainwater Killifish and Mysids from Art2.

Tiny fish bloom with the Mysids. Little fish either eat the Mysids or feed off the same tiny food as they do.

Unfortunately, many of our tiny fish are non-native, like the Rainwater Killifish shown above.  But overall, the Mysid bloom is one of the best early omens of a good fish year.


Tiny Corbula at Coy4

Bad News!  Corbula bloom too!!!! There were hundreds of tiny Corbula at stations Coy2 and 3, and especially Coy4 on December 7th.  This pulse of recruitment also appears to immediately coincide with the first big rains.


We don’t usually find such small Corbula.  This cluster of demon-spawn couldn’t be more than weeks old.  Larval Corbula must have emerged from the upstream river channels as the rains hit.  Rainwater surges flushed them downstream where they settled down.

Hopefully, armies of diving ducks and bottom-feeding fishes will clean up these little monsters soon.


Slightly bigger (normal-sized) Corbula from Coy1

As always, adult Corbula are found a few miles upstream; mainly at station UCoy1 and all along Alviso Slough.

Think of Corbula as the “anti-Mysid.”  They efficiently suck up all the phytoplankton, ciliates, and copepod neonates that otherwise feed our Mysid blooms.  If Mysids starve, the marsh starves.


Better News:  Giant Longfin! (top).  This is a Longfin-zilla from the first trawl in Pond A21.  Longfin Smelt, like the endangered Delta Smelt, generally live a year or two. They grow to about 100mm after two years.

Winter rains were a little late this year.  Accordingly, Longfins are arriving a little later.  Only 26 of them were caught in December trawls.  We are hoping the numbers pick up soon.


Giant Longfin #2.  Another giant Longfin in Pond A21. (bottom fish).  This second big one measured close to 130mm.  The fish above it is a fairly normal-sized Longfin.

The two big fish caught this day may be in their third year.  This could be an important finding.  Most Longfins don’t survive long enough to get so big or so old.


Longfin Smelt caught the next day, December 8th, in Pond A19.  Shown here in the Photarium.

All but two Longfins in December were caught in restored salt ponds A19 and A21.  The other two were caught in Dump Slough (South Coyote Slough) which itself was a restoration project completed in 1988.  Had there been no habitat restoration in this area, would be seeing Longfins here at all?


American Shad from station Art3 on 8 December.  Salinity averaged 16ppt: roughly the brown-to-green threshold.

American Shad also return with the rain – as discussed at length earlier in December.  And, they turn brown.  (I found one web page that mentions the Shad color change: colors darken to a brownish shade when they enter freshwater to spawn.”)

The above reference again mentions that East Coast American Shad return for spawning after roughly five years at sea.  In contrast, our Shad return every year.  Most returning shad here are very small, (young-of-year) at about 100mm, or 4 inches.  But, we occasionally see older ones close to 200 and 300 mm.

American Shad are fast swimmers.  I presume most of the big fish outrun the trawling net.


2. Anchovy Color Update

Young Blue Anchovies in the deep Lower South Bay (stations LSB1 & LSB2).

The Anchovy color scheme continues to loosely follow the Shad Rule reported earlier this month (see previous Fish in the Bay report


  • Anchovy chromatophores do not express brown color. Gold is as far as they go when water is fresh:  In upstream areas where Shad turn rich chocolate brown, Anchovies become clear/colorless, which looks pinkish or brownish to the casual eye, and
  • Anchovy chromatophores practically disappear (fade away) in fresh or brackish water over time.


Juvenile Anchovies

Baby Anchovies (juveniles) are translucent and colorless up to a certain age.  (What age?  Possibly a month or two?)  Only the largest juvenile in the top left panel shows a flash of green in the crown.  Those smaller than about that size show no color whatsoever.  Colorful chromatophores, either blue, green, or gold, develop in the crown of the head and then express themselves along the lateral line.  What determines the color that the fish shall express???

The dorsal side seems to remain translucent and largely colorless unless the fish migrates farther out to the deep Bay or ocean (much speculation at this point).  Otherwise, the general color rule for Northern Anchovies remains:

  • Blue = high salinity,
  • Green = mid-range,
  • Gold = low salinity.


Blue-green Anchovies at two upstream stations.

Bluish-Green Anchovies at Art2 and A19.  The selection of anchovies from stations Art2 and A19 shown here are show consistent the blue-green color of mid-range salinity.

This is a devilish problem:

  1. Salinity changes rapidly with sloshing tides in tidal marshes such as these. It can change by minute during ebbs and floods.  It changes with depth.
  2. Anchovies colors change slowly, if at all.
  3. Shad change fast! I could swear I have seen some shad change from brown to green as they sat in a tray.  I will attempt an experiment next time.


Anchovy color mix in the fresher side of Pond A19.

Anchovy colors are never completely consistent in these waters.  Others caught on the upstream (usually fresher) side of the Pond (station A19-1), were a mixed bag of golden-greens and blue-greens.

  • Have these golden-greens been hanging out in fresh surface waters?
  • Did this dark blue-green recently swim in from a saltier place?
  • Do any, or all, of these young fish migrate out sea where they become fully blue or green-backed at some point?

Their recent life-history is written across their backs in bright neon colors.  We just need to break the code!


3. Crangon Shrimp on the Move!

Black and Brown-tailed Crangon at LSB1

Crangon also move with the change in seasons.  According to literature, shoreward migration of adult female Crangon is triggered by a drop in temperature.

Also, high salinities at end-of-year allow Black-tailed Crangon (C. nigricauda) to penetrate farther into Lower South Bay before the rainy season freshens it up.

However, there may be a fuzzy boundary between C. nigricauda and C. franciscorum. 


Nearly identical Crangon at Coy4; one with black tail (telson), one with brown tail.

We often see dark-tailed Crangon this time of year.  The tail, or “telson,” is sometimes half-way between C. franciscorum brown and C. nigricauda black.

Example #1: Above – Identical shrimp; one with black tail the other brown.  Are they really two different species?  Are these Black-tails (C. nigricauda) or regular Crangon (C. franciscorum)?


Dark-tailed Crangon?

Example #2:  Crangon with gray or dark brown tails. Do C. franciscorum telsons also darken up at higher salinity?  Or, do C. nigricauda telsons sometimes turn brown?


More dark-tailed and brown-tailed Crangon from station Coy1. 

Example #3:  A mixed bag of practically identical shrimp: some are telsons are almost black, some are clearly brown.  Do we know our Crangon?  Are these C. franciscorum? C. nigricauda? or both?


Dark-tailed Crangon from Artesian Slough.

 Black-tailed Crangon in Artesian Slough?  If it weren’t for the far upstream location, I would not hesitate to classify these as C. nigricauda.  Also, the two different sizes strongly suggest that these are different year classes.

Mysid Note:  Allen informs me that large juicy mysids in the photos above may be the “Neomysis kadiakensis” variety, to the best of his naked-eye discrimination.

N. kadiakensis is the principal mysid variety in the North Bay that was studied in this Dean, Bollens, Simenstad, and Cordell (2004) paper: 

  • I gather from the paper that large female Mysids may perform a bayside-to-marsh brooding migration similar to what we see in Crangon shrimp.
  • The paper’s introduction provides a good short summary about why we should care about Mysids: Recent declines in the abundance of mysids and the closely correlated declines in the abundance of their predators further point to the trophic importance of mysids in the San Francisco estuary (Feyrer et al., 2003).”
  • So far, Mysids do not appear to have declined in the Lower South Bay / Alviso Marsh Complex. This may explain why this area has “some of the highest density and diversity of fish species remaining in SF Bay.” (Dr. Hobbs, perscom)


C. franciscorum from Coy4

Regular brown-tailed Crangon (C. franciscorum) adults are staging in Lower Coyote Creek.  The franciscorums shown above appear to be females with growing egg masses (yellow or tan areas just behind the head), but they are not yet berried (carrying eggs).  Unfortunately, numbers are much reduced this year: roughly 1,000 Crangon this month, versus almost 9,000 in December 2018.

This time last year, massive numbers of berried female C. franciscorum were caught at most stations.  It was “The Great Crangon Brooding Event” – the only one I have ever seen.

According to a few different sources, Crangon may be “protandrous hermaphrodites,” with males changing into females after their first year.  IF TRUE, it may explain a couple of things:

  1. Most Crangon caught after March or April 2019 were small – ranging around one to 1.5 inches. Presumably these tiny ones are offspring from last year’s Great Crangon Brooding Event. (Are they all male at this point?)
  2. Suddenly, we are seeing large numbers of two-inch Crangon with yellow heads (egg masses). I am guessing that these are two-year-old females of a previous generation that have just migrated in.
  3. We still see some smaller Crangon alongside the larger ones, but I suppose most of the young-of-year generation (all males?) have now migrated out to the deeper Bay hopefully to return as females next year.


4. A few signs of continued high salinity.

Ctenophores amongst Crangon at Coy3

Ctenophores, or Comb Jellies, appear as clear bubbles in the photo above.  70 were caught this December weekend, including 26 upstream of the Railroad Bridge.  These marine creatures usually do not venture to this far south into the Bay.  Higher salinity and cool temperatures seem to bring them in.  (We also saw these in November.)


Decorator Crabs at LSB2.

Decorator crabs!  We caught 6 Decorators on Saturday!  They are also infrequent marine visitors in Lower South Bay.  Again, they were likely brought in with higher than normal salinity at the end of the year.


5. Flat Fishes

California Halibut, right-eyed and left-eyed, from Lower South Bay stations.

California Halibut continue to show up.  These are more young recruits spawned by the “Warm-water Blob Generation” of adults that hatched in 2014-2015.

We continue to see a near equal mix of right-eyed (eyes on right side of head) and left-eyed Halibut.  I have not taken the time to document exact percentages.  Literature says California Halibut populations have a 60/40% left/right-eyed split.  We seem to be pretty close to that ratio.


English Sole from Coy4

English Sole.  We typically see very small English Sole starting in January.  This one was an “early bird.”  And, it is the largest one we have ever caught here.  It is still small by English Sole standards, but a record for us, nonetheless.


Large Starry Flounder from UCoy1 on November 10th.

Starry Flounder flashback.  We recently caught our biggest Starry in November, but I wasn’t able to post the photo at the time.  This monster measured at 410mm – standard length.  However, Starries can get much larger; to at least double that size.  I am pretty sure this one is a reproductive female returning to spawn in the creek.


Starry Flounder from Pond A19 on December 8th.

Usually, we see small Starries about this size or slightly larger: ~180mm – standard length.  Supposedly, they can be reproductive even when so small.

November through about February is the Starry spawning season, at least it was near Monterrey Bay when this Orcutt (1950) report was prepared for CDFW (Fish Bulletin No. 78):  The author notes that spawning Starries appear to “seek shallow water near river mouths and sloughs.”


I have more to report … another installment.

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