Fish in the Bay – July 2021: Anchovy & Goby Season – Crangon Disappeared!

Trawl map.

Good News!  The summer 2021 Anchovy spawn continues.  And, we found more bryozoan reef and two new interesting creatures at LSB1: a worm and a sponge.

Bad News!  Other than Anchovies, some Mudsuckers, and a few extra baby Starry Flounder, overall fish counts dropped as summer warmed – which is normal.  …. But, Crangon shrimp practically disappeared!  That is not normal!


Bay-side stations trawling results.

Anchovy spawn.  We found egg-bearing females and/or milting males at 18 of 20 stations in July.  Almost the entire Lower South Bay is again an Anchovy Spawning Zone!


Upstream of Railroad Bridge.

Summertime low Dissolved Oxygen (DO). DO readings are always a highly-variable bag of readings.  In June, DO was low almost across the board at upstream stations.  In July, readings were more mixed.

Low DO fish.  We caught a lot more Longjaw Mudsuckers in July (31 total).  Yellowfin, Arrow, and Cheekspot Gobies are also doing well in this Low DO season as explained further below. 


1. Anchovies!!!

Schools of Anchovies!  Shoals of small fish periodically appeared on the side-scan sonar/fishfinder as we cruised along the main stem of Coyote Creek on Saturday.  Since Anchovies were the only fish we netted in large numbers, it’s a safe conclusion that these blotches on sonar were Anchovies.


The Anchovy total was 1349.  That is very good for a July, but we have seen better. 

As always, Anchovy dorsal colors varied from blue and green to golden.  Golds are invariably caught at upstream stations; blues and greens are more frequent closer to the Bay. 


Spawning season.  Anchovies were in a high state of spawning readiness.  Only a few ‘egg-checks’ were performed at each location.  Egg-bearing or milt-emitting fish were observed at all stations except LSB2 and Art1 where no Anchovies were collected.


Green-back and Blue-back Anchovies at Alv3.  We continue to surmise that long-bodied vivid blue and green-backed Anchovies are recent arrivals from the ocean.  Anecdotal observations seem to support this.


Golden Anchovies at Art2.

Artesian Slough is the home of the Golden Anchovy!  Golden and Golden-green Anchovies predominate at all upstream stations, but water in Artesian Slough is persistently freshest owing to the discharge of treated wastewater from the San Jose-Santa Clara Regional Wastewater Facility (SJ-SC RWF).  Here, the Anchovies are consistently the most golden. And, they spawn here too! 


Green Anchovies (at bottom) amongst many golds and golden-greens at Art3.

A few vivid blues and greens were netted in a largely golden-brown population as far upstream as Coy1, Art3, and UCoy2. 

  • It is still unclear if Anchovies of different colors and age classes freely mix with each other or if these are representatives of different schools of fish that have been consolidated into a single trawl catch.
  • Random egg-checks at all stations detected eggs or milt regardless of the dorsal color of the examined fish. 


A rainbow of Anchovy colors from green (top) to gold (bottom) at UCoy1.

Anchovies are more numerous at the upstream marshy portions of Coyote Creek, and they tend to be more golden-green in that area.  It is clear that many of the green anchovies ‘brown-down’ in fresher water.

Do blue Anchovies also “brown-down” as they acclimate to fresher water at upstream stations?  If this is happening, it is much harder to detect from monthly trawl catches. Blue Anchovies do fade considerably in fresher water.  But, blues generally look a little different: more silver and longer-bodied than greens and golds. Anchovy dorsal color is highly variable, but some aspects seem to persist for the lifetime of the fish.  

Do Golden Anchovies “blue-up” as they migrate back to the ocean?  I continue to think that this does not happen. The golds don’t appear to have blue chromatophores whatsoever.  But, who knows at this point?


2. Shrimp Wars.

Palaemon Shrimp at Coy1.

Palaemon explosion.  The dry year has been very good for Palaemon shrimp; we have counted 19,168 year-to-date.  This is already a 10-year record-breaker. 

As shown in the photo above, most of the Palaemon in July were pregnant!  (Females with egg broods appear to have a dark gray mass under the abdomen when viewed from above.)  We have always seen a mix of big and tiny egg-bearing Palaemon through the warm season.  A quick review of literature reveals that this is a very common Palaemon characteristic. Palaemon females begin brooding eggs as new recruits later in the same summer that they hatch; they then over-winter and produce at least two successive brood the following summer. 

Palaemon Science: the two papers cited below discuss different Palaemon species and summarize general lifecycle characteristics.

Kim and Hong (2004). Reproductive Biology of Palaemon Gravieri (Decapoda: Caridea: Palaemonidae).

From the abstract: 

  • “Breeding period was seasonal, beginning in March, peaking in May (89% ovigerous females), and then ending by August. Females with embryos near hatching had ovaries filled with vitellogenic oocytes ready for new spawning, indicating successive spawning.”
  • “Females reached sexual maturity and produced a brood in their first year, overwintered, and produced a bood again the following summer.”  

Guerao and Ribera (1995). Growth and Reproductive Ecology of Palaemon Adspersus in the Western Mediterranean.

From results and discussion:

  • “… recruitment took place in both males and females. By August and September the new recruits to the population formed a cohort, clearly distinct from the older individuals in the population.
  • Female maturity clearly began in December, … The ovigerous females carrying embryos at stage 3 (eggs about to hatch) appeared in March. The spawning period lasted until September and the percentage of ovigerous females reached a maximum in April and June.  
  • Some of the early specimens … in summer (yearling individuals) reached sexual maturity and laid eggs at the end of the reproductive period in August and September, together with prawns [sic] of the previous generation (wintering individuals).
  • As in other species of Palaemon, … the growth rate of males was much lower than that of females.
  • … the sex-ratio found herein was skewed in favour of females … Baden and Pihl (1984) showed that the female prawn generally dominated in the shallowest waters, where he recorded a female:male ration of 88%:12%. … Depth seems to influence the relative occurrence of the sexes …”

Breaking the Palaemon code:  I used to call the big egg-bearing females “Dragon Queens.”  Until now, we couldn’t figure out why both big and small egg-bearing females were commonly caught together.  Now we know!


Palaemon Shrimp at Alv1.  There are at least two “Red Dragon Queens” in this bunch.  (year old females)

Palaemon turn reddish in saltier water.  This may be a result of diet: brown algae and other marine phytoplankton contain fucoxanthin pigment.  Whatever the cause, the reddish/brownish color is a reflection of the slightly higher salinity in Alviso Slough where these were caught. 

  • This bunch was a mix of young and old shrimp. Many here were also berried with eggs.


Palaemon Shrimp at Coy2.

Station Coy2 is roughly half a mile downstream from Coy1.  Many of the Palaemon at this station were on the larger side and NOT pregnant.  These may be spent females between their summer broods.  Kim and Hong (2004) mentions that females molt after each egg release.  Many of these shrimp are large (female) with clear appearance – possibly recently molted?

All catches of Palaemon included pregnant females, but the proportion seems to shrink as we proceed downstream.


Micah and I calibrate our shrimp counting trays.

We caught over 1,300 Palaemon at Coy2.  This was not the most shrimp we have ever seen at a single station, but it is a lot.  When we get caught in a shrimp traffic jam like this, we adapt our counting method to ensure maximal survival for all fish and bugs. Big piles of Palaemon slowly suffocate as they sit in the tray

In this instance, Micah and I counted shrimp into handfuls, then handfuls into trayfuls.  Roughly 300 Palaemon filled each tray about 1/3 full.  The count is tallied, and the shrimp are immediately released. 

Even though they are non-native, Palaemon shrimp are important here:  Seals, Sturgeon, Bat Rays, and Leopard Sharks depend on them as food, especially now that Crangon are scarce.  We do not kill Palaemon absent any clear research purpose!


Crangon shrimp (center) in a tray full of Palaemon.

Crangon Population Crash!  Perhaps the worst news of all:  Crangon shrimp numbers dropped from almost 1,900 in June to only 93 in July!  Droughts are not good for Crangon.  Even so, a disappearance of this magnitude was unexpected.  We hope that young Crangon simply migrated out to sea.

I speculate another possibility:  Young Crangon may have undergone a molt.  Small recently molted Crangon could be very vulnerable to predation from a large population of adult Palaemon.  It is just a thought at this point.


3. Bat Rays and Flatfishes.

Bat Rays.  Only 6 Rays and 3 baby sharks were caught this month.  It was not a great month for elasmobranchs, but it’s just luck of the trawl.    

  • Bat Ray dentistry.  We decided to do a quick dental check of two rays this month.  Bat Rays have very strange-looking teeth they use for crushing clams and snails that they eat. Literature refers to them as “pavement teeth.” 
  • According to Wikipedia:  “Bat ray teeth are flat and pavement-like, forming tightly-packed rows that are used for crushing and grinding prey—the crushed shells are ejected and the flesh consumed.”


California Halibut and Starry Flounder.  We encountered one young Halibut and 11 baby Starries at Coyote Creek stations Coy1, Coy2, Coy3, and UCoy2. 

  • Starries always prefer the deeper main channel of Coyote Creek especially when they are most abundant in late summer and fall. They do venture into the smaller side sloughs and ponds, but not as frequently. 


4. Goby World.

Arrow and Cheekspot Gobies.  The year-to-date catch of a combination of native Arrow and Cheekspot Gobies is 393.  The 2021 Arrow + Cheekspot count is already a 10-year record.


Arrow and Cheekspot gobies continue to be combined as one category.  These tiny gobies grow to about 1.5 inches max. They are hard to distinguish by naked eye.  They can also be easily miscounted as young Yellowfin Gobies or “Unidentified Gobies” so the 10-year record is encouraging but could be influenced by improvement in our identification skills.

Yellowfin Gobies.  We caught 358 Yellowfins in July.  This has been a good year so far, but 2015, 2016, and 2017 were better years for Yellowfins.


Bay Goby (Lepidogobius lepidus). A single Bay Goby was caught in July, but this is very good news.

  • Bay Gobies used to be the most common native goby in this area.  They declined and practically disappeared for a few decades.  We caught only 19 of them in 2012, only one in 2014, 2015, and 2018, and ZERO! In all other recent years. 
  • Then, something wonderful happened!  We counted 31 tiny babies in February and March of 2020.  The 2021 count is up to 33 and we are catching slightly bigger ones!  Are Bay Gobies returning? 


Longjaw Mudsuckers.  31 young native Mudsuckers were counted in July.  (These are also gobies.)  Mudsuckers can breathe air for hours when dissolved oxygen concentrations drop in the brackish marsh.

  • It is always a joy to see them. Mudsuckers are the sentinel species that indicate presence of healthy pickleweed marsh.  


Micah examines the Mudsuckers between trawls in Pond A21.


5. The Reef.

Encrusting Bryozoan Reef expands!  For the last year, we reported observations of a Bryozoan reef at LSB1.  This month, we encountered rocky Bryozoan outcroppings along the shallow western bank of the deep channel at LSB2 as well. 

Bryozoan are a different phylum from coral, but they form very similar-looking calcium carbonate hardscapes on the estuarine bottom. The irregular coral-like growths provide sheltered habitat for many small marine creatures.    


Decorator Crabs.  We caught 18 Decorator Crabs in July: all but one were found at LSB stations.  We caught a total of 30 in 2020, but this is the first sighting of Decorators in 2021.  These spindly marine crabs hide in rocky crevices. Camouflage is their main defense. 


Yellowish, irregularly-shaped Bread Crumb Sponge attached to a piece of encrusting bryozoan.  LSB1, 3 July 2021.

Bread Crumb Sponge (Halichondria bowerbanki)This is a common sponge on pier pilings in Central and North Bay, but we have not seen it before in LSB. 

  • Bad News: The Bread Crumb Sponge is not native here, but it has been endemic in the northern parts of San Francisco Bay since at least the 1950s. It probably arrived with commercial oyster shipments over a century ago.  It originates from the North Atlantic region. 
  • Good News: This sponge doesn’t seem to do any harm.  Like any sponge, its only purpose is to filter water.  Overall, the sponge is probably beneficial here. 
  • See: Mooi et al. (2007) Animals of San Francisco Bay, A Field Guide to Common Benthic Species, California Academy of Sciences, p. 21. 


New Polychaete!  We spotted a new long and skinny worm (see top panel).  This worm resembles the more familiar “Nereid Polychaete” (aka ‘pile worm’ or ‘rag worm’) we see so often except that this one is much smaller and skinnier. This is worm may be common on the Pacific coast, but its identity has us flummoxed.  Can anyone identify the worm shown at top?

Scaleworm (Harmothoe imbricata or “Fifteen scaled worm”).  At least six Scaleworms were observed in July.  These are very common marine polychaetes, but we rarely saw them in LSB trawls prior to 2019. … Worms are usually good.

  • See Mooi et al. (2007) Animals of San Francisco Bay, A Field Guide to Common Benthic Species, California Academy of Sciences, p.98.  

    By far the most commonly encountered scaleworm in San Francisco Bay, Harmothoe lives nestled in crevices where oxygen is limited, necessitating added ventilation. This is accomplished with ciliary tracts between the scales and body wall. Scaleworms are active carnivores, preying upon amphipods and other small animals using an eversible proboscis equipped with 4 hooked jaws. Harmothoe survive in both low and high salinity environments. Sexes are separate, with pair-bonding during the breeding season. Fertilization occurs under the scales, where eggs are brooded until the planktonic larvae are released.

    … Importance to humans:  Studies on endocrine control of reproduction suggest usefulness as a bioindicator of climate change.  Other biochemical studies include serotonin and its effects on scale bioluminescence.” 

6. Weeds.

Peppergrass.  The non-native peppergrass (Lepidium latifolium) explosion continued in July. The spread of this noxious, but highly edible weed is probably fueled by this year’s extreme dryness.  Less drought-tolerant native marsh plants cannot compete against it on higher ground above the waterline.  We saw a lot of it on the high ground above Dump and Alviso Sloughs.

  • DON’T EAT IT!!!  Although every part of Lepidium is edible, the South Bay Salt Pond Restoration Project is coordinating herbicide spraying with resource agencies to control invasive Paspalum ( and other noxious weeds that threaten native plants and habitats in restored wetlands.  Peppergrass is not specifically targeted at the moment but likely will be soon.  Birds probably poop on Lepidium anyway.  Always wash your vegetables and know where they came from!   
  • Save the Bay article about reseeding restored areas with native marsh plants during current drought conditions:  


Bird Nests in the California Bulrush.  Certain birds hang their nests in tall tules.  Unfortunately, in this extreme drought, the tallest tule, California Bulrush, has been knocked back almost everywhere. 

There are only two places where bulrush still stands tall this year:  Artesian and Dump Sloughs.  I shot the above photo montage of some of the nests we saw hanging in Dump Slough.  Micah confirmed that these are Marsh Wren nests, as indicated by the enclosed roofs and tiny entrance holes.  


7. Seals.

Harbor Seals.  On July 3rd, lower high tide had begun to ebb, and most of the redder adults were still out on the hunt during our first pass by the seal rookery.  Seals on the beach were mostly gray pups with spotted coats.

New behavior observed:  During June and July visits, on four or five occasions we noticed a big seal randomly making a big splash while swimming near the colony.  I asked SF Bay Seal-expert, Denise Greig, what this was about. She confirmed that “tail-slaps” are a common behavior: “Tail slaps are very likely males showing off to other males to maintain the social hierarchy.  In theory, this dictates which male has access to the females,” according to Denise. 

When the big seal slaps, all the moms and pups on the beach immediately turn and take notice.  Other seals, probably younger males, seem to watch warily as they swim nearby.

Notes from long-time Harbor Seal researchers:  Both Denise Greig and Sarah Allen sent me materials discussing the science and history behind our San Francisco Bay Red Seals:

  • Sarah Allen et al. (1993). Red-Pelaged Harbor Seals of the San Francisco Bay Region.
    From Abstract: “Elemental analysis of hair samples revealed that red coloration was from deposition of iron oxide precipitates on the hair shaft” 
  • Marilyn J. Fluharty (1999). Summary of Pacific Harbor Seal, Phoca vitulina Richardsi, Surveys in California 1982 to 1995. Table 2 reports results of annual aerial surveys performed during summer molting season. 
    • Site 204 is Calaveras Point – this is our Seal rookery.
    • Site 205 is Mowry Slough – this is the bigger colony in Lower South Bay, just a few miles to the north.  
  • Kopec and Harvey (1995). Toxic Pollutants, Health Indices, and Population Dynamics of Harbor Seals in San Francisco Bay, 1989-1992. Moss Landing Marine Lab Technical Publication 96-4 – See p.20: (Denise sent this as a pdf. Unfortunately, no link is available.)
    “The oldest records of harbor seals in San Francisco Bay come from the extreme south Bay, in the area around Mowry Slough. Bonnot (1928) reported the observations of a CDF&G field agent who in the–1890s participated in seal hunts at “extensive rookeries in the South San Francisco Bay near Alviso”. In 1927 and 1928, field engineers surveying the marsh and installing equipment along Mowry Slough for the Alden Salt Company reported 75 and 100 seals, respectively, at Calaveras Point, though it was noted that Mowry Slough was also a place of refuge for the seals.”    

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