Fish in the Bay – February 2024, Part2. Freshwater Flush, continued.

This is part two of the February blog. 

The February flush and the resulting salinity drop scattered most of our fish catch far downstream.  Overall fish numbers declined from January, but totals are still good compared to past years.  


1. Longfin Smelt Staging for the Spawn.

Longfin Smelt Spawning Ground.  This marks the third year that mature Longfin males have concentrated at a fairly specific part of Coyote Creek at Station UCoy1. A palm tree growing on the side of the Newby Island Landfill marks the spot.   There are other spawning sites spread around the upstream trawling area, but this one appears to draw the densest concentration of males.

What features attract Longfin males to select a time and place for spawning?  In addition to cool temperature and low salinity, most literature states that spawning Longfins seek “sandy, or gravel substrates, rocks and aquatic plants (Moyle 2002).” 

Add clam shells?  There are practically no sandy or gravel substrates in this area. The bottom at UCoy1, and all other LSB stations, is soft mud with hydrozoa and clam shell hash.  Dead shells and plant roots are the main hard substrates here. 


Longfin Smelt count = 375.  The overall Longfin count was very good for a February.  Nonetheless, the freshwater flush greatly reduced numbers at all upstream stations with exception of UCoy1.

  • Longfins at the UCoy1 spawning ground were again overwhelmingly mature males with just a few big females. There were no juveniles in this bunch.   
  • Longfin spawning in Coyote Creek marshes has become more regular and robust since its first reported discovery in 2019:

The Longfin count remained steady at UCoy1 despite being exposed to the most extreme salinity drop and fiercest flushing flows. 

  • UCoy1 January Longfin count: 31. Salinity was ~8 ppt.  Temp was ~13 C.
  • UCoy1 February Longfin count: 30. Salinity was ~0.3 ppt.  Temp was ~11 C.


Pond A19 is one of the alternate Longfin spawning sites.  At this location, four mature males outnumbered one female and one juvenile. 

Pond A19 was the only other upstream station where more than a single Longfin was found in February. 

  • Pond A19 January Longfin count: 63. Salinity was ~14 ppt.  Temp was ~12 C.
  • Pond A19 February Longfin count: 6. Salinity was ~5.4 ppt.  Temp was ~12.5 C.


Once again, restored Pond A21 hosted the majority of Longfins in February.

Females and juveniles stage where food is plentiful farther downstream.  Large mature males are present but comprise a much smaller portion of the population.  Some Longfin spawning may also occur at downstream sites. 

Longfin numbers at downstream stations declined moderately, from 467 in January to 338 in February, example: 

  • Pond A21 January Longfin count: 280. Salinity was ~17 ppt.  Temp was ~12.5 C.
  • Pond A21 February Longfin count: 260. Salinity was ~15 ppt.  Temp was ~13 C.

Conclusion:  The large decline in Longfin catch at all upstream stations other than UCoy1 suggests a few things:

  1. Some factor, other than salinity and temperature seems to have brought an earlier end to Longfin spawning season than we saw in 2022 and 2023.
  2. Spawning Longfins are not impeded by salinity as low as 0.3 ppt nor strong flushing flows – at least in the short term.
  3. UC Davis researchers analyze otoliths, gonads, livers, and stomach contents from selected Longfins to hopefully reveal the secrets of this spawning ground.



2. Other Fishes.

Northern Anchovy count = 60.  The Anchovy count dropped considerably after atmospheric river rains freshened up LSB.  All but several of the February Anchovies were tiny babies that likely hatched a few to several months ago in these very marshes. 

Pacific Herring count = 11.  Herring numbers also dropped.  As in previous months, all Herring were still young-of-year at around 70 to 80 mm standard length. 


Clupeiform colors in February.  Herring dorsal colors are always slightly browner compared to adult Anchovies at any given level of salinity. 


California Halibut count = 7.  A total of 38 Halibut were caught in January and February.  All were tiny babies measuring from 26 to roughly 60 mm standard length.  Halibut are a warmer water “El Nino fish.”  These babies seem to be a result from an El Nino spawn. 

Like all flatfishes, Halibut hatch as fairly normal-looking two-sided fish. Very soon after hatch, one eye migrates to the other side of the head as the Halibut metamorphosizes into the flatfish we recognize.   


Bay Pipefish count = 18.  We caught a lot of pipefish at downstream stations during these February trawls.  This is early and unexpected in a wet year.  The Pipefish count usually starts increasing in March or later during dry years.


Saddleback Gunnel count = 1.  A single Gunnel was caught at station Coy2. Salinity was only 10.6 ppt (surface) and 11.2 ppt (bottom) at the time. 

  • So far, all four Gunnels in the last few years were caught in January or February – the freshest time of year!
  • Do Gunnels seek fresh water?


Striped Bass count: 3.  We caught two large Striped Bass in Artesian Slough and one baby Bass at Coy4. 


Sturgeon Alert!  A large Sturgeon was detected on sonar just upstream of station Coy1.  He looked very Sturgeon-like in both “down imaging” and “side scan” views.     



3. Bugs

Corbula Clam count:  699.  This was an unpleasant surprise.  Almost 500 of them were picked up at station Alv1 alone. 

Like many estuarine creatures, Corbula recruit and flourish from rainwater flushing.  They concentrate where fresh river water meets the salt.  These clams tolerate a wide range of salinity, but they do not survive well against the many competing organisms in a higher salinity environment farther downstream.

  • An army of diving ducks in winter and Bat Rays in summer help control this non-native scourge.
  • However, barnacles, tunicates, and maybe Philine snails may put a bigger dent in Corbula populations. Investigation continues!


Shrimp Wars.

Palaemon count = 562. Palaemon shrimp numbers will bounce back as weather warms. Palaemon populations can outcompete native Crangon during dry years.  They get beaten back in wetter years.

Exopalaemon count = 206. Exos are fresher water cousins of Palaemon shrimp. They always concentrate in the upstream ends of creeks and sloughs.   

Crangon count = 608.  The year-to-date total for Native Crangon shrimp is already about 8,500.  Many of them were again gravid this month.  That is a good start.  These additional spring rains should help baby Crangon recruit well again this year. 


Upogebia count = 8.  All Upogebia were caught in the main stem of lower Coyote Creek, aka “Shrimp Alley:” two at Coy2, five at Coy3, and one at Coy4.

These Mud Shrimp are non-native “Upogebia major.” Dr. John Chapman at Oregon State University concluded as much from photos taken during the previous Upogebia stampede in January 2022: 

We still do not know why Upogebia appear to occasionally flee from their deep burrows beneath the marshes.  Two possibilities:

1) Upogebia could be escaped bait. However, the local Laine’s Bait shop sells a different variety, called “Ghost Shrimp” (Neotrypaea californiensis.)    Or,

2) Upogebia flee their burrows when salinity drops precipitously after big rains.


Upogebia are extremely beneficial ecosystem engineers that have a huge impact on nitrogen cycling.  D’Andrea et al ( 2009) Geochemical ecosystem engineering by the mud shrimp Upogebia pugettensis … Density-dependent effects on organic matter remineralization and nutrient cycling.

  • We must understand these mini-lobsters.


4. Birds

Tricolored Blackbirds at Dump Slough.  Once or twice a year we spot this small flock of Tricolors in the tall Bulrush.  Both Red-winged and Tricolored Blackbirds use upland freshwater marshes for feeding and nesting.     


Marsh and farmland habitat was developed within eyesight of this area in just the last 30 years.  So far, these last remaining Tricolors keep returning.      

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