Fish in the Bay – July 2020, Anchovy Alert! Anchovies are spawning in Coyote Creek!

This is a Fish in the Bay special Alert:  Anchovy spawning has been confirmed in Lower South San Francisco Bay.

SF Bay map highlighting Lower South Bay (LSB).

It has long been known that Anchovies spawn somewhere in San Francisco Bay. Fine net surveys past and present consistently collect larval Anchovies and eggs in the central portions of the Bay nearly year-round.  Even at our Lower South Bay monitoring locations, Dr. Jim Hobbs has collected very young juvenile Anchovies and eggs on different occasions.

So, we know Anchovies must spawn somewhere in the Bay.   We just have not verified an exact location … until now!  


Trawl map highlighting the July Anchovy Spawning Zone.

The trawl map shows Anchovy numbers at each station on the Bay side (downstream of the Railroad Bridge) and the much larger total numbers of Anchovies on the upstream side.

Our July Anchovies preferred fresher-brackish water: Of the 2148 Anchovies caught at all 20 stations, 73 percent, were upstream of the RR Bridge, in and around Lower Coyote Creek.  And, that does not count another 291 at station Alv2 – again upstream in fresher water.


Water quality parameters at the 10 trawling stations where reproductive Anchovies were observed.

A total of 1556 Anchovies were caught on the upstream side in warmer, fresher, and in a few instances somewhat oxygen depleted water. 

  • Upstream salinities varied from 1 to 12.9 ppt, with bottom salinities reaching as high as 21.2 at Coy1 (only 18 Anchovies caught Coy1).
  • We found Anchovies with eggs at all stations on the upstream side (indicated by blue box).
  • Highest Anchovy numbers (1465 out of the 1556 total) were found at stations nearest the main stem of Lower Coyote, exclusive of Stations Coy1, Art1, and Dmp1 on the periphery. (Concentrated Anchovy zone is indicated by green circle.)
  • Female Anchovies with eggs were found at all stations on the upstream side.

Anchovies are not known to migrate to such warm, fresh, deoxygenated water. Northern Anchovies are supposed to prefer spawning in ocean salinity around 35 ppt.  They are also supposed to prefer much cooler temperatures for spawning.  What is going on here?


Anchovy numbers in relation to 6+ years of monthly trawling data.

BTW:  We are having a very good Anchovy Summer!  The July 2020 Anchovy catch was one of the four highest since consistent monthly monitoring at all 20 stations began in January 2014.

This SF Examiner article briefly explains Northern Anchovy offshore booms, busts, and politics:


Anchovy collage from Pond A19.

Anchovy color investigation continues.  As reported last year at this time, adult Northern Anchovy dorsal colors gradually shift from green to gold or brown as summer progresses.

This color shift follows the basic Clupeiform salinity scheme we identified over the past year:

  • Higher salinity = bluer tones,
  • Mid-salinity = green,
  • Low salinity = brown (for Shad) or gold (for Anchovies).
  • Additionally, Northern Anchovies lose all iridophores with long-term exposure to low-salinity water to become clear/brown-backs.


Blue-backed Northern Anchovy caught at Coy4 on Saturday.

It is still possible that strong blue or green dorsal colors in some adults may indicate separate migrating and breeding populations, but the majority of green-backs/gold-backs appear to be all one interbreeding population in which dorsal color loosely corresponds with in-Bay or in-marsh salinity.


Anchovy eggs discovered.  As we counted and measured tiny Mississippi Silversides, Three-spined Sticklebacks, Top Smelt, and Anchovies at our first station on Sunday, we noticed that Anchovies seemed unusually well-fed and plump.   Gentile pressure on the abdomen of one specimen revealed eggs ready for dropping.


We soon realized that many, if not most of them, were pregnant females.  We also found a few males that appeared to be full of milt.

From literature, we learn that:

  • Northern Anchovies can spawn year-round depending mainly on temperature.  Off the Coast of most of California there is a spring spawning peak followed by a smaller late fall peak.
  • Females release batches of eggs every 7 to 10 days.
  • Males fertilized by broadcasting milt.
  • Eggs hatch in 2 to 4 days, depending on the temperature of the water.
  • In all species of Anchovy, females usually drop eggs in the hours around midnight.
  • Availability of food greatly affects the size and frequency of spawn and success of recruitment.

Selected Anchovy Spawning Literature:

  1. NOAA Fisheries, Northern Anchovy page:
  2. UCSD California Sea Grant, Nothern Anchovy page:
  3. Egg and Larval Production of the Central Subpopulation of Northern Anchovy in the Southern California Bight. NOAA Fisheries, 2016:
  4. The Spawning Energetic of Female Northern Anchovy, Engraulis mordax. Roe Hunter and Roderick Leong, Fishery Bulletin: VOL. 79, NO. 2,1981
  5. Spawning, fecundity, hatch-date frequency and young-of-the-year growth of bay anchovy Anchoa mitchilli in mid-Chesapeake Bay. Zastrow, E. D. Houde, L. G. Morin,  Chesapeake Biological Laboratory, Marine Ecology Progress Series, Vol. 73: 161-171, 1991
  6. Spawning frequency of the anchovy Engraulis capensis. C. Melo. (1994) South African Journal of Marine Science, 14:1, 321-331.
  7. Racial and Seasonal Variation in the Pacific Herring, California Sardine and California Anchovy. Carl Hubbs, Online Archive of California, 1925
  8. Recent collapse of northern anchovy biomass off California. Alec D. MacCall, William J. Sydeman, Peter C. Davison, Julie A. Thayer, Farallon Institute for Advanced Ecosystem Research, 2015
  9. Northern Anchovy, Engraulis mordax, Spawning in San Francisco Bay California, 1978-79, relative to Hydrography and Zooplankton Prey of Adults and Larvae. Michael F. McGowan,   University of Miami, Fishery Bulletin: VOL. 84. NO.4. 1986.


Unfortunately, we did not have the time, nor research funding and mission, to make detailed observations.  I could only snap as many photos as possible of egg-bearing females after counting and measuring.  Then, these frisky fish had to be tossed back to marsh waters.

No one wants to disrupt a good spawn!


Anchovy size and dorsal color had no correlation to reproductive readiness in our observation.  We found greens, golden-greens, and golds full of eggs.  Most pregnant females seemed to be smaller, perhaps 50 to 70 mm, and golden-green.  But, we also found females with eggs up to 100 mm long and with both green and golden-green dorsal color.


We captured what information we could with limited time.


Anchovy colors continued to roughly correlate with salinity.  The most golden and golden-brown Anchovies were found in furthest upstream stations.  But, even at those locations, one or two bright forest-green Anchovies would show up.

I continue to believe that these iridescent colors are telling us where the Anchovy has been.  In this case, the bright green ones must have just arrived from the deep Bay, or perhaps the deeper ocean.

Imagine one day being able to read these fish like a book!


Golden Summertime Anchovies.  Our summer Anchovies seem to concentrate in shoals as close to freshwater sources as they can.  Salinity of somewhere around 10 to 15 ppt must be preferred because that’s where highest Anchovy concentrations seem to be.

Literature tells us that Anchovy egg production increases with temperature and especially food availability.  Anchovy ovaries are continuous year-round egg-producing machines under ideal conditions.

To my mind, the corollary is that egg production must make females powerfully hungry.  They will swim any distance, endure freshwater, and suffer in low Dissolved Oxygen, as long as they find food to support the egg-production machine.  … This may not be a great hypothesis, but I am going with it for now.


Every batch of Anchovies at each station had at least a few egg-bearing females.  And, we could only examine a small minority.


Males extruding milt seemed to be relatively rare.  I suspect that the Anchovies we examined on Sunday were predominantly female.  But, given the limited random sampling, it is only a thought.  Plus, it is much harder to see the milt.


Micah Bisson measuring fish from Artesian Slough.

We counted 3203 fish of all types on Sunday!  And, almost 4000 the day before. (Plus, more than 18,000 Crangon over the July weekend!)

So far, this is a very good fish and bug summer.


The brownest Anchovies were again found in Artesian Slough.  Anchovies transition from gold to brown/gray/colorless as their iridophores disappear in fresher water.  Artesian slough conveys constant freshwater discharge from the San Jose-Santa Clara Regional Wastewater Facility, so Anchovies turn into true Brown-backs.


Station Art3 often has the highest number of Anchovies during summer and late fall months.  Now we know they spawn here too!


We found quite a few females with eggs in Artesian Slough.

Clearly, something about the brackish-freshwater attracts these spawning Anchovies.  Food, in the form of phytoplankton, copepods, mysids, and/or amphipods is the best attractant I can think of.


Golden Anchovy from Artesian Slough.

It is very satisfying to find golden Anchovies.  It’s even better when they are part of a spawning population.


I must acknowledge and thank:

  • Levi Lewis for managing the UC Davis Otolith Geochemistry and Fish Ecology Lab and supporting the Lower South Bay Monitoring Program.
  • Jim Hobbs for designing this monitoring program and compiling years of data describing the biological complexity of this ecosystem.
  • Micah Bisson for maintaining and prepping the boat and counting close to 3,000 fish while I took photos on Sunday.

Absent their years of sampling and study, Human World may never have learned that Anchovies spawn in Lower Coyote Creek! 

Now we know!

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