Fish in the Bay – September 2021: Operation Guadalupe.

Hello folks.  From mid-August thru mid-September, the UC Davis OG Fish Lab did something very different.  With additional funding from San Francisco Estuary Institute (SFEI), the UC Davis researchers conducted an augmented trawling survey of Guadalupe Slough and surrounding Bay, sloughs and creeks. 

Operation Guadalupe.  Guadalupe Slough was the main focus of this effort.  But, all slough and creek segments were given comparable treatment. 

  • 17 stations were surveyed (see map above).
  • Each station was trawled on four different dates from mid-August to mid-September.
  • Three 5-minute trawls were conducted in series at each station for each monitoring date.

This scheme of three successive “triplicate” trawls allows evaluation of statistical variability in trawling effort in addition to providing more information about fish and bug distributions up and down the LSB marsh complex.  


Operation Guadalupe begins.  L to R:  Me, Micah, Alec Scott, & Sammy Araya.  Team members Ian Slack & Leticia Cavole not shown.  (photo by Eric Larkin of Western Sea Kayakers.)

For this blog post, I will only cover Guadalupe Slough & LSB trawls. 

Part I: Guadalupe Slough.

Guadalupe Slough History.  Once upon a time, Guadalupe Slough was the mouth of Guadalupe River.  But, the river was redirected to adjacent Alviso Slough in the 1870s.  At some later point, several smaller creeks (e.g., Calabazas, Saratoga, and San Tomas Aquino Creeks) that did not originally discharge to the Bay were connected to Guadalupe Slough through a series of flood-control channels.  The other major freshwater flow to this slough comes from City of Sunnyvale’s Water Pollution Control Plant at the location shown in the above map. 

Nearby restorations:

  • In 2011, Pond A6 was breached to open tidal exchange between the lower end of Guadalupe and Alviso Sloughs. Sediment has accumulated in Pond A6 and new marsh has formed and continues to grow.
  • In subsequent years, the “Pond A8 Complex,” comprised of former salt evaporator ponds A5, A7, A8, and A8S, was opened to allow controlled tidal exchange.

The trawl plan for Guadalupe is shown above.  Stations are numbered Guad1, Guad2, and Guad3 from upstream to downstream.  The rough location of each 5-minute trawl is indicated on the map by a line roughly 600 to 800 feet in length.

This was the first time we otter trawled Guadalupe Slough in at least 9 or 10 years.  We really did not know what kinds of fish and bug populations to expect.    

Results …

Mudsucker and Anchovies, Guad1, 5 Sept


To be honest, I did not expect to see many fish in this slough because of its limited connections to adjacent marshes.  Happily, I was wrong.  Finding many egg and milt-bearing Anchovies during the high point of this current spawning season was our first delightful surprise. 

  • For some reason, the Anchovies were most numerous at Station Guad2 during all four trawling events.
  • Many large “Big Mamas” with dark and colorful dorsal sides were conspicuous.

Big Mama Anchovy (top) and younger one (bottom), Guad3, 5 September.

Anchovy colors and size.  The number of big (>90mm), dark, and colorful (blue and green) Anchovies that were caught at Guad2 was immediately noticeable.  These Big Mamas are always a small minority of the total Anchovy catch, but they are very important for our spawning success.


For most species of fishes, Big Mamas produce thousands of eggs compared to the youngsters.  As noted in earlier blog posts, the Big Mama Anchovies seem to be more prevalent near the mouths of sloughs and creeks, present but uncommon farther upstream, and rare at Deep Bay stations.

  • Anchovies are sequential spawners. Eggs are released at roughly weekly intervals.
  • Egg production requires an enormous supply of protein.
  • Ergo, Big Mama Anchovies migrate to areas of high food production like heat-seeking missiles during the spawning season!


Quick field identification of Anchovy age, origin, and sex is still largely a guess unless or until limited otolith or genetics studies can be done. 

  • Length increases with age, but growth rates will vary greatly with temperature. (And, as Carl Hubbs documented in 1925, warmer temperatures in Bay and estuarine waters stunt Anchovy growth.)
  • Dorsal sides darken with exposure to sunlight. Presumably, this darkening occurs in clear ocean waters and less so in turbid creeks and sloughs.  
  • Dorsal hues are influenced by salinity but color intensity varies greatly by light angle. In this instance, we interpret these blue and green fish as having recently moved from the higher salinity Deep Bay into Guadalupe Slough.  But, scientific confirmation is still lacking.


More than a few Big Mama Anchovies in this bunch, Guad2, 5 September.

Despite the uncertainty, Anchovies in Guadalupe Slough were definitely bigger than those caught at the Lower South Bay (Deep Bay) stations on the same days.  This is very encouraging!


Another Big Mama Anchovy: big, dark, blue & green-backed. Guad2, 22 August.

A total of 915 Anchovies were caught over four trawling dates in Guadalupe Slough. 

  • This was not a record-breaker as slightly more were caught in comparable trawls of Alviso Slough and the main stem of Coyote Creek – particularly at station Coy3 where 1398 anchovies were caught.
  • Nonetheless, Operation Guadalupe revealed that Guadalupe Slough is supporting a decent population of spawning-ready Anchovies. (But, do they actually spawn here?  That is the next question!)


Baby Bat Rays!!! 

Micah measures a baby Bat Ray at Guad2 on 5 September.

Baby Bat Rays were the second delightful surprise.  Apparently, either mama bat rays swim into the lower Guad to deliver babies, or the babies themselves migrate upstream into the slough.  Either way, the area around station Guad2 is a significant baby bat ray haven. 

  • The magnitude of this baby bat ray blowout is difficult to comprehend. Over the entire month-long Operation Guadalupe trawls, 132 out of 304 Bat Rays (42 percent) were caught in Guadalupe Slough alone.
  • Guadalupe Slough is baby Bat Ray central!!! (Particularly station Guad2)


Leopard Sharks.

Sammy showing a young Leopard Shark from Station Guad3, 5 September.

Leopard Sharks require high salinity.  Low and variable salinity keeps them away from upstream creek areas in Artesian, Dump, and Upper Coyote Sloughs.

  • The mouth of Guadalupe Slough is close enough to marine waters of Lower South Bay to encourage young sharks to swim upstream as far as Guad2.  
  • For Leopard Sharks, Guadalupe ranks #5 out of the eight Bay, creek, & slough segments surveyed.


Arrow & Cheekspot Gobies.

Guadalupe Slough hosted more native Arrow and Cheekspot Gobies than any other segment!  Both Arrows and Cheekspots were more prevalent at Station Guad2.

  • Of the two gobies, Cheekspots were the bigger surprise. Only 10 Cheekspots were caught in all other Bay, creek, and slough segments combined compared to the 106 collected in Guadalupe Slough. 
  • Granted, variability was high: many Cheekspots were present on August 22nd and Sept 5th. We saw only 2 Cheekspots on August 26th and 4 on Sept 9th.   


Cheekspot Gobies with pregnant fat bellies.  Guad2, 5 September.

Most of the Cheekspots at Guad2 had pregnant fat bellies! 


Striped Bass.

Sammy examining a Striped Bass caught at station Guad1 on 5 Sept.

Striped Bass tend to be rare in late summer due to the heat.  Only ten were encountered during the entire month-long Operation Guadalupe trawling effort. All were caught in upstream, slightly fresher water segments.  Half of them were caught at station Guad1 alone!


One large Starry Flounder – A Big Mama.

Sammy releasing the Starry Flounder back to Guad3 on 5 September.

Starry Flounder.  The only Starry caught in Guadalupe Slough was the big mama shown above.  Starries swim up into creeks to spawn in late summer and fall.  We usually catch smaller ones, 4 to 6 inches in length.  This Starry was a big one for us. 


Summary of trawling catches – Guadalupe Slough.

Salinity Gradient. 

  • Corbula clams either like slightly fresher water, and/or they are very vulnerable to predation by Bat Rays, and probably Philine and Oyster Drill snails as well. Either way, Corbula get scarce as water gets saltier in the Slough.
  • Palaemon Shrimp, at least at this time of year, greatly prefer downstream/saltier areas. We saw this trend in all slough segments, but the trend was particularly clear in Guadalupe Slough.

Effluent Gradient.  We detected a likely wastewater gradient for four fish species that preferred Guad2 nearest the Sunnyvale Plant:  Anchovies, Arrow/Cheekspot Gobies, and Bat Rays.   We guess that production of phytoplankton, amphipods, and/or copepods near the Sunnyvale effluent is attracting these native fishes.  


Guadalupe Slough is #1 for Bat Rays, Striped Bass, & native Gobies!

It was very gratifying to find the highest numbers of Bat Rays and native gobies in Guadalupe.  This portion of Guadalupe Slough is only about 3 slough-miles long, but it packs an ecologically beneficial punch from a fish perspective.   


Gold Star for the Sunnyvale Water Pollution Control Plant. 

This Gold Star of Wastewater Treatment Excellence goes to the Sunnyvale Water Pollution Control Plant.  More of at least 4 native fish species were found near Sunnyvale’s treated wastewater than anywhere else in LSB in August-Sept 2021.  

The native fishes have voted!  There is no higher Water Quality standard.


Part II, LSB Trawls.

Red Ceramium mess on 5 September.

Red Ceramium continued to clog the trawl net at downstream stations throughout August and September.  We have never seen a sustained bloom of this fine, hair-like algae before in over 10 years of trawling.  For better, or for worse, it greatly altered the bottom habitat from LSB to stations as far upstream as Guad3, Alv3, and Coy1.  


Bat Rays and Leopard Sharks.

Alec Scott (left) and Sammy Araya (right) showing off some of the catch at LSB stations during Operation Guadalupe.


Bugs in LSB.

There was a Greater diversity of bugs (mollusks) on the bottom at LSB.  This was not unexpected.  There is always a wider array of benthic invertebrates at Deep Bay stations owing to the constant near-marine levels of salinity.  Unfortunately, practically all of those shown above are non-native invaders.   


Chameleon Gobies.

Chameleon Goby, LSB2, 5 September.

Chameleon Goby.  Only 5 Chameleons were netted at LSB1 and LSB2 and only on September 5th.

Chameleons are the high-salinty cousins of Shimofuri Gobies, so we usually only find these at LSB stations.  Upstream in the sloughs, Shimofuris have been experiencing a massive population explosion, particularly in Alviso Slough since June.  Whatever is stimulating Shimofuri population growth has had no impact on the Chameleons.


Some oddball critters.

Barred Surfperch at LSB1 on 22 August.

Barred Surfperch.  This was the only surfperch of any type caught during Operation Guadalupe.  Barred Surfperch are common on the coast, but they are rare oddballs in LSB. 

  • Shiner Surfperch are more common here, but we caught NO Shiners during these trawls.   


Pregnant male pipefish, LSB, 5 Sep.

Bay Pipefish.  We caught a pregnant male pipefish at LSB1 on 5 September.  Pipefish are common in the marshes, but we never caught them far out in the middle of LSB – until now. 

  • Dense mats of Ceramium red algae may have provided refuge for this animal.
  • Why else would a pipefish venture so far out in the Bay?


Anemone Mystery.  Throughout Operation Guadalupe we occasionally picked up a few small anemones (roughly 1 cm in diameter) at almost all stations.  Some were orange, some were green.  Some were firmly attached to hard substrate like shell, rock, or wood.  Many were loose and round-bottomed.

Deep thoughts about anemones.  We began documenting small orange anemones exclusively at LSB (Deep Bay) stations a few years ago.  They have now spread far upstream.

  • We presume these anemones are native Diadumene franciscana, but D. lineata is another possibility. High salinity during this dry year likely facilitated their spread upstream.
  • During Operation Guadalupe, we found many anemones that were detached and round-bottomed. They appear to propagate by rolling around with the sloshing tides.
  • Initially, all detached specimens appeared green in color suggesting a different species. But, by September we found several orange specimens that were also not attached to any substrate.
  • Are these one species or two? Are they native?  Are they a good sign, or bad?        


Summary of trawling catches – LSB.

Compared to Guadalupe Slough, LSB catches were slim for all species other than a few marine bugs. 

  • Granted, the narrow channel of Guadalupe Slough tends to concentrate species where a trawl net can more efficiently grab them.
  • Nonetheless, these results, and common sense, tell us that Guadalupe Slough is an important upstream segment of the entire Lower South Bay ecosystem.


Random Bird Photos during the Guadalupe Slough runs.

Various piscivorous birds seen: Osprey, Brown Pelicans, & Tern on August 22nd, and American White Pelicans on 5 September.

Our fish continue to feed charismatic birds at all times of year.

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