Fish in the Bay – February 2023, Freshwater Flushing Continues.

Cold rain continued to fall as Atmospheric Rivers blew in from the ocean throughout January and February, and even through March. 


Low salinities caused by rainwater flushing resulted in smaller fish catches.  The pulse of freshwater pushed all marine species farther downstream into the deep parts of LSB or out even farther north and out of LSB altogether.


Ironically, and most welcomely, threatened Longfin Smelt are strongly attracted to freshwater flushing.  Males continue to stage at the spawning grounds far upstream on Coyote Creek while females and young loiter downstream near the creek mouth – see discussion farther below.


1. Freshwater Flush Observations.

Benthic bivalves tend to get clobbered by big salinity shifts.  We picked up basketfuls of dead shells from upstream stations.  Most shells were probably long dead and just scoured up from the flushing flows, but many were also freshly dead.

Surface-dwelling Musculista mussels and Corbula clams were hit hardest.  We found freshly dead and dying animals at upstream ends of both Alviso and Coyote Creek sloughs.   These non-native invaders are always present.  Big salinity shifts like this one help keep them under control.


I learned from USGS reports and data, that phytoplankton in the bay usually experiences only one big “Spring Bloom” each year.  During a spring bloom, chlorophyll-a increases to between 15 to 50 ug/l and sometimes much higher in the deep parts of the Bay.  The typical baseline chlorophyll count in the main stem is usually closer to around 5 ug/l.  The bloom can happen anytime between December to May and lasts only a few weeks.  

Presumably, phytoplankton and chlorophyll densities are much higher in warmer and shallower upstream marshes. Looking from above, water in Alviso Slough and restored ponds A19 and A20 looked brown and very turbid.  Upwelling clouds of particulate material were very conspicuous in the ponds when winds and currents were dead calm on February 18th and 19thThese ponds are probably Diatom factories when the Sun shines!

This interesting paper, Cloern, et al (2010), describes a relationship between PDO and NPGO ocean cycles and three marine indicator species in SF Bay (English Sole, Dungeness Crab, and Black-tail Crangon, along with phytoplankton abundance) whose populations increase or decrease in synch with those cycles.


In both January and February, there was a strong green-to-brown delineation in Artesian Slough.   A steady freshwater source from the SJ-SC RWF feeds the upstream end, and consequently, the water is very dark and clear. 

  • Bright green billowy clouds of either microscopic Euglenids or Chlorophytes show up by mid-day when the Sun is out.
  • But, the water’s appearance changes abruptly roughly a mile downstream where tides mix and salinity rises. The water turns brownish and muddy looking, possibly indicating the dominance of Diatoms.   

The secrets of marsh productivity, fish and bug health, river flows, and possibly even ocean cycles lie in the murky colors of the water.  We must train our eyes and our instruments to read this!


2. February Fishes.

                    The 6 American Shad from Pond A21 began changing from green to brown as we watched.

American Shad.  These beautiful non-natives arrived in California by train from the East Coast in 1871. They spawn in the Sacramento and San Joaquin River systems.  We only see youngsters here.  I probably said this many times, but it bears repeating, the American Shad scientific name, ‘Alosa sapidissima,’ literally means “the delicious Shad.”  A lot of people like fishing and eating them. Historically, they are a very important fish.

Dazzling iridescent guanine crystals along their backs ‘green up’ in mid-to-high salinity (above 10 ppt) and ‘brown down’ at lower salinity.  The water was saltier on the bottom of Pond A21 when these were caught (14.8 ppt).  As we poured them out of the net into a bucket of fresher ambient surface water (10.4 ppt) their green backs began changing to brown almost immediately.  How cool is that?

Also mentioned before, Shad easily shed their scales.  Hence you see “Shad glitter” in the tray.  The glittery scales are used as chaff to confuse a charging predator at the crucial last seconds.  These mirror-bright fish are designed to run fast and not be seen underwater.

                                                                  Threadfin Shad from Pond A21

Threadfin Shad.  Only four Threadfins were caught.  These are the smaller, deeper-bodied cousins of American Shad.  Threadfins were introduced to California around 1953.

Salinity color change is something that all Clupeiforms can do.  But, Threadfins seem to raise the camouflage game to another level. …

It always strikes me how Threadfin dorsal colors look almost identical, but also very different from American Shad depending on light angles.  Threadfins have a golden mirror overlay that blocks color as angles change.  It confuses both my eye and my camera, which I suppose is the point.  This must be the best underwater camouflage that evolution could perfect over tens of millions of years. 


Northern Anchovies.  All 42 Anchovies caught in February were very young larvae or post-larval juveniles.  As for many other creatures, the freshwater flushing at least temporarily pushed Anchovies into saltier water farther downstream.


California Halibut. One juvenile and two nearly larval Halibut were netted. Young Halibut feed and recruit in LSB throughout the year. At least a few adults swim into LSB to broadcast spawn each winter.  Halibut larvae drift for a few weeks after hatch.  They then settle on the bottom to feed and grow big enough to migrate back out into the deeper Bay.

English Sole.  24 young English Sole were caught at LSB stations.  Unlike Halibut, English Sole adults spawn off the coast.  Sole larvae deliberately swim toward fresher water and linger in LSB between December through May for recruitment and feeding. They spend the rest of their lives in marine coastal waters.


Yellowfin Goby. Most of the 18 Yellowfins caught in February were females with bulging bellies.  Classic baby fish month is coming in April. That’s when most of the baby Yellowfin and Arrow Gobies hatch.  Yellowfin adults swim downstream from fresher water for their spawn.  Most males are currently hidden in mating hollows and caves waiting for the egg-laden females to show up.

Staghorn Sculpin. Staghorns perform the same mating ritual a month or two earlier.  Most of the Staghorn hatch occurs from December through March, hence most of the 30 we saw in February were tiny juveniles.

Longjaw Mudsucker.  Only 2 Mudsuckers were seen in upstream marshes.  They are less active during cold months.  They tend to shelter in small creeklets at all times, so we rarely catch more than a few dozen even in warm months. 


Other young fishes.  Very young flatfishes and Staghorn Sculpin are typical catches this time of year.

Bay Gobies.  The two caught this month were a welcome surprise. We keep hoping that native Bay Gobies will re-establish in LSB, but after several years of waiting, it appears that is unlikely to happen.  A few young ones show up each spring, but they fail to recruit in any substantial numbers.  This is probably due to competition and predation from non-native Yellowfin, Shokihaze, and Chameleon/Shimofuri Gobies. 


                                             Pacific Tomcod.  Four more were caught at downstream stations.


3. Longfin Smelt

                                                 American Shad (top) with four female Longfin Smelt at Alv2

295 Longfin Smelt were caught in February.  This is our second biggest February catch, exceeded only by the much higher number (895) last year. 

Longfin Smelt were rare wintertime visitors when UC Davis trawls began in 2010.  Until 2017, a previous big rainwater flush year, there were no signs of Longfin spawning behavior here.

Then it all changed after the first big Freshwater Flush of February 2017. 
Somehow Longfins (re)discovered (largely restored) marshes near the mouth of Coyote Creek.  After that year, first a few dozen, and then many hundreds of spawning-ready Longfins were observed every winter from December through March or April. 


The most interesting behavior we see now is the sharp sexual segregation in Longfins during their spawning migration.  This tendency of males to stage upstream was first deduced from statistical analysis of the catches up to 2019. (See: Hobbs et al (2019) submitted as 2018-19 Annual Report for DWR Contract # 4600011196 – sorry no link!) 

  • Now, in every winter trawl, we clearly see that nearly all Longfins in the fresher waters near UCoy1 are ready males showing prominently bulging belly flaps and long anal fins.
  • Female Longfins are relatively scarce at UCoy1 but comprise the majority at most downstream stations where they appear to continue to feed and swell with eggs.


Longfins at the UCoy1 Spawning Ground.

  • As mentioned last month, Longfin males appear to cease feeding when in spawning mode.  This may apply to females as well. It could be an evolutionary adaptation that prevents Longfins from cannibalizing their own eggs and young.
  • In this photo, the second fish from the top left is likely a spent female – she looks just as hollow-bellied and emaciated as all the other males.


Bad news: Longfin parasite.  Longfin Smelt are victimized by the same Cymothoid isopod gill parasites (aka “Devil Bugs”) that inflict Shad, Tomcods, and many other fishes.  It is not known what impact this parasite has on our recovering Longfin population, but we keep an eye on it.  One bad parasite can ruin an excellent fish recovery!


4. Interesting Crustaceans.

Crangon shrimp numbers remain disappointingly low.  In a good year, we have seen up to a few thousand Crangon females full of eggs loitering in saline waters (above 20 ppt) at downstream stations.  The released young migrate into fresher water for feeding and recruitment.  Dry years tend to suppress Crangon shrimp (the local brown-tail variety). 

This current freshwater flushing should feed a good Crangon recruitment and increase populations.


                                                                 Pair of Gammarid amphipods in Pond A19.

Gammarids.  In January and February trawls, we came across three or four Gammarid pairs like this.  The larger male holds a female with his front legs in apparent mating behavior.  Interestingly, the male tends to hold onto his female even after capture and handling.

Gammarids (aka “Scuds”) can be difficult to identify to species.  Apparently, the classification scheme has been reorganized in the last decade or so, see: and  

These amphipods build small burrows for protection.  They are also omnivorous; eating epiphytic algae off rocks and plants, but they also readily ambush and eat larval fishes and shrimps.  They are also highly desirable food for bigger fishes and shore birds.  This short YouTube video shows a burrowing pair at work: 


5. Ducks!

Upper photo: Ducks over Pond A19. – Lower photo: 10,000-duck-day on Pond A18. 

  • Around 2015, I noticed that up to 10,000 dabbling ducks and coots can now settle on Pond A18 on a good spring day. That was not possible when the pond was hypersaline and used for salt production. 
  • After A18 and the adjacent ponds A16 and A17 were breached for circulation in 2005, visiting duck numbers rapidly increased.  I had always hoped that duck numbers would continue to increase forever.  But, the last few drought years discouraged them a bit.  Now they are back!
  • Big Rain = Lots of Ducks!

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