Fish in the Bay – February 2024, Freshwater Flush & a Later Red Tide.

February trawls were conducted on 10 and 11 February just after two atmospheric rivers dumped a good amount of rain. 


The Big Flush dropped salinity to below 6 parts per thousand (ppt) at all stations on the upstream side. 

Both fish and shrimp counts also dropped.  Critter counts typically decline after a big flush due to the combination of strong flushing flows and large drops in salinity.   

  • Anchovies, Herring, Adult Crangon Shrimp and other salt-tolerant species were pushed far downstream and out into Lower South Bay.
  • More interestingly, the big flush brought us a few freshwater “oddballs” like Sacramento Suckers, Pacific Lampreys, and Common Carp.


Good News:  Restored Pond A21 was again the big winner in providing habitat for threatened Longfin Smelt.

This first part of the February report focuses on the upstream end.


1. Mysids after a Big Flush.

Mysid Bloom.  Mysids are tiny shrimp-like crustaceans roughly 1 centimeter long.  They live in coastal and fresh waters all over the world. Mysids tend to bloom here in early spring after big rains. 


Mysids are sort of like miniature krill.  They feed on smaller phytoplankton and crustaceans, like copepods and cladocerans. Mysids are, in turn, eaten by practically all larval and adult fishes.  Even Gray Whales along the coast depend on Mysids as a preferred food.


2. Micro-world in February. 

Janai Southworth joined us in February.  She collected samples at upstream stations and provided the imagery shown below.

Terpsinoe musica.  “The silica bars between the valve inflations are distinct and appear as “musical notes”. …Terpsinoë musica is widely distributed and can be found in freshwater to marine habitats (Wehr 2003). …  It has been suggested that T. musica is most frequent in hard waters with warm temperatures (Sterrenburg 1994).”

  • Luttenton et al. (1986) sampled several substrates in Cummins Spring in Oklahoma and found that musica was the most abundant on submerged tree branches, and was abundant on roots and aquatic bryophytes.
  • … a specimen by Stephen P. Main collected from the National Tropical Botanical Garden falls pool in Kauai illustrated the presence of musica along with Pleurosira laevis

Pleurosira. “Pleurosira laevis is typically a halophilic and rheophilic species but can survive in lake environments.”

Melosira. “… remain free-floating planktons  for a certain stage in their life cycle. The genus has cosmopolitan distribution and inhabits both freshwater and marine habitats.” 

Rotifers. Tiny soft juicy food for tiny fishes.

Testate amoeba. Perhaps slightly harder food??  “Testate amoebae can be found in most freshwater environments, including lakes, rivers, cenotes, as well as mires and soils.” 


Cylindrotheca (Diatom). “Cylindrotheca also has many marine representatives, all typical of benthic mudflats …”   

Oscillatoria (Cyanobacteria).  “Filamentous cyanobacterium which is often found in freshwater environments, such as hot springs, and appears blue-green.  Its name refers to the oscillating motion of its filaments as they slide against each other to position the colony facing a light source.” 

Polychaete worm.  “Polychaetes are segmented worms that live in nearly all marine habitats, from the shallow seashore or estuaries to the deep sea. … Many species of these worms—and there are at least 11,500 species worldwide—perform ecological functions similar to those of earthworms, their terrestrial relatives.”,colored%20or%20bioluminescent%20%3A%20bristle%20worm 

Copepod.(/ˈkoʊpəpɒd/; meaning “oar-feet”) are a group of small crustaceans found in nearly every freshwater and saltwater habitat. Some species are planktonic (living in the water column), some are benthic (living on the sediments)…” 



Gyrosigma (Diatom).  “Frustules of Gyrosigma acuminatum are large and distinct. It is primarily an epipelic species which lives unattached on fine substrates. This species is considered to be globally distributed in freshwater but has also been observed in brackish habitats.” 

Surirella (Diatom). “… are common in the benthos, especially epipelic habitats, across a wide range of water chemistry. Cells may be relatively small, to very large (a few hundred micrometers), depending on the species. Because of the extensive raphe system, species of Surirella have high motility as compared to other diatom genera. They are able to live within sand grains and fine sediment and can move through the sediment by means of the raphe system.”

Pediastrum (Chlorophyte).  “… a genus of green algae … that inhabits freshwater environments.”  


Aulacoseira (Diatom). “… is one of the most common freshwater diatom taxa, especially abundant in plankton of lakes and large rivers. One of the most successful species of freshwater centric diatoms, … The genus was resurrected to separate freshwater Aulacoseira from Melosira, a primarily marine genus.” 

Gloeocapsa (Cyanobacteria). “… from the Greek gloia (gelatinous) and the Latin capsa (case) is a genus of cyanobacteria. The cells secrete individual gelatinous sheaths which can often be seen as sheaths around recently divided cells within outer sheaths.

Microcystis (Cyanobacteria).  “… is a genus of freshwater cyanobacteria … Communities are often a mix of toxin-producing and nonproducing isolates.”

  • Note: Some folks may be alarmed by the appearance of cyanobacteria, particularly by Microcystis which can exude toxin.  However, these cyanos did not appear to dominate Janai’s samples.  Cyanos often flush out of freshwater creeks under strong flow conditions.  Fish and bugs appeared healthy.  Overall, our planet cannot survive without cyanos!


3. Side note: Red Tide Alert at Lake Merritt – 7 March 2024.

As I was working on this February blog report, a red tide briefly appeared in Lake Merritt on March 7thThis caused great concern amongst those of us who remember the Great Fish-Killing Red Tide of July-August 2022 at the same location: 

In 2022, the red tide organism was positively identified as the Raphidophyte, Heterosigma akashiwo, a tiny mixotrophic species that sometimes blooms in warm estuarine water when salinity, sunlight, and stratification are notably high, i.e. typically in late summer/early fall.

As of mid-March, the culprit behind this latest red bloom has not yet been identified. Both H. akashiwo and another microorganism, Mesodinium, were reported to be present.  Either one alone can cause water to turn brick red. 

Two usual Red Tide suspects:


4. Fish that flourish during a freshwater flush.

Two Common Carp at Art1, 11 Feb 2024.

Common Carp count: 4. Carp are very common non-native fish in the rivers and creeks just upstream of the salty waters where we trawl.  But, we had never caught one in ten years of trawling until after the big rains in early 2023.  Now, we are catching them fairly regularly.  Is this a Carp population explosion?  Or, are these just more stragglers that are being washed downstream? 


Threadfin Shad (far left and top right) and American Shad at Art3.

American Shad count: 25.  Threadfin Shad count: 28.  The overall Shad count was roughly average: These non-native fishes generally like freshwater flows. This February count was low compared to recent years but very high compared to any year prior to 2018.


Starry Flounder count: 66.  We first saw a big surge of tiny baby Starries last May.  They grew progressively bigger each month. 

Starries are now even bigger and probably reproductive at this point.  Like many other fishes, Starries migrate upstream every year to spawn in fresher waters. These could be the very same babies we saw in May! 


Sacramento Sucker count: 2.  Suckers are a common river fish in California.  They were a dietary staple for Native Americans a long time ago.  Suckers don’t usually drift far enough downstream for us to catch them in monthly trawls except when freshwater flushing is particularly strong. 


Pacific Lamprey count: 2.  Lampreys are slippery boneless fishes. They are hard to catch in the net or hold in the hand.  We hope and assume our Lamprey counts are gross undercounts.  Two were caught in regular monthly trawls in February plus five more during Broodstock trawls the previous week. 

We presume that a Pacific Lamprey is shown above. However, her teeth were too small for positive identification. 

Prickly Sculpin count: 1.  Pricklys show up after big rains. They are one of the few partially “catadromous” fishes we catch.  Catadromous means they live most of their lives in freshwater creeks and migrate downstream to spawn and hatch their young.,generally%20a%20bottom%2Ddwelling%20species

Micro-world is very complex & subtle. 
Ana Vidovic plays Asturias by Isaac Albéniz …

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