Fish in the Bay – September 2021: Operation Guadalupe, Part 3.

Operation Guadalupe trawl stations.

Operation Guadalupe. Continued.  For this third and last installment, we surveyed the upstream tidal end of Coyote Creek. Coyote Creek splits and loops around both sides of the Newby Island Landfill at this point:  Upper Coyote slough flows on the east side and Dump Slough on the west.  A third slough, Artesian Slough, emanates from the San Jose-Santa Clara Regional Wastewater Facility and joins just downstream of the split.


Part III.   The Upper Coyote Segment: Upper Coyote, Dump, and Artesian Sloughs.

Trawl map annotated with local historical restoration sites.

The above map shows the rough locations of each trawl at the six stations.  Each slough segment was assigned two trawl stations.  A series of three 5-minute trawls were conducted at each station on four dates.  (5 minutes x 3 x 4 = 60 minutes of trawling effort.)

  • Fish and bug numbers summarized above are adjusted to a 10-minute Catch Per Unit Effort (CPUE) for comparability with regular monthly trawls. (Total/6).  All other numbers reported in this report are raw totals from the month-long survey.
  • Blue-green map annotations foreshadow the following tale of destruction and recovery. 


Brief History of this Area.      

The original marshlands.  The south-eastern corner of San Francisco Bay was covered in Pickleweed, Spartina, and Alkali Bulrush marsh until the late 1800s.  Salt evaporator ponds were first leveed off from existing marsh on the north side of Coyote Creek in the late 1800s through 1930s.  Then, from the 1930s through the mid-1950s, salt evaporator ponds numbered A6 through A21 were carved out, leveed off, and converted to salt evaporation.

After Pond A18 was leveed off by the Leslie Salt Company around 1955, only Triangle Marsh remained as one of the last remnants of original salt marsh.


Until 1956, raw sewage from expanding human population flowed to an increasingly barren wasteland.

Raw Sewage!

Raw sewage flowed into Coyote Creek via Artesian Slough until 1922.  Then from 1922 to 1956, they had two long concrete pipes to flow untreated sewage directly into Coyote Creek at the western corner of Triangle Marsh. The landward boundaries of Triangle marsh were defined by the sewer pipes and the railroad track.  Bay waters around this location became anoxic and foul-smelling.  The problem had become so acute by the 1950s that the public demanded wastewater treatment as a solution.

1956 The San Jose-Santa Clara Water Pollution Control Plant was constructed.  At time of construction, the San Jose facility provided primary treatment only, but plans and financing were in place to add secondary (biological) treatment by 1964. Chlorine disinfection was added in 1971.  Nitrification and filtration treatment was added in 1979.  Over subsequent decades, each advance in wastewater treatment resulted in a corresponding recovery in Bay water quality.

  • See Yigzaw (2016): “…the data show major load reduction in BOD, TSS, and nutrients corresponding to Facility improvements. … anoxia and hypoxia were virtually eliminated following the Facility’s upgrade to nitrification, significantly improving DO concentrations in the LSB.”
  • An increasing volume of fresh and ever cleaner treated wastewater flowed through Artesian Slough. 


Artesian Slough: station Art1, on September 4th, 2021

Four decades of small-scale recovery and restorations followed. 

1970s: Artesian Slough. A new marsh sprouted along the banks of Artesian Slough.  This marsh was dominated by California Bulrush in the vicinity of the freshwater effluent emanating from the SJ-SC RWF.  This fresh to brackish marsh attracted birds.  By the late 1970s, the 2-mile length of Artesian Slough was designated a critical and protected nesting habitat for herons and egrets. Larger marsh birds simply had nowhere else to roost in the local area.


1980s & 90s: Upper Coyote and Dump Slough.  Restoration and flood control projects in the late 1980s restored small patches of upstream tidal marsh habitat upstream on Coyote Creek.

  • 1986 – The 260-acre Coyote Creek Lagoon was opened. This was the earliest sizable tidal marsh restoration in the local area. This combination of vegetated marsh, mudflat, and slough channel joins Coyote Creek with Mud Slough.
  • 1988 – The Coyote Creek bypass Channel was widened. This flood control project, managed by the Santa Clara Valley Water District, converted a narrow drainage ditch into 100+ acres of tidal and upland marsh through which “Dump Slough” flows. 
  • 1999 – CDFW determined that nesting habitat in Artesian Slough no longer required seasonal protection. Herons and egrets had discovered new and better places to roost!
  • These experiences indicate it takes roughly a decade for local salt marshes to substantially recover.


Pelicans and gulls in Pond A19 on 4 Sep.

2000s:  Salt Pond Restoration Project.  Altogether, six large former salt ponds in the Upper Coyote tidal area were opened to circulation with Bay water in 2005 and 2006.  Together, these ponds comprise over 1600 acres

  • 2005/2013 – Ponds A16 and A17 were initially opened for controlled muted circulation in 2005. After some reconfiguration work in 2013, both Ponds were reopened to provide bird nesting habitat under managed circulation.
  • 2005 – Pond A18, owned by City of San Jose, was opened for controlled muted circulation.
  • 2006 – Ponds A19, A20, and A21 were simply breached to allow passive tidal restoration. By the late 2010s, Ponds A20 and A21 (210 acres) were nearly completely revegetated in dense spartina and pickleweed habitat.  As of 2021, Pond A19 is roughly 50 percent vegetated with spartina and some pickleweed.
  • by 2011, UC Davis researchers began documenting fish and invertebrate species recolonizing restored salt ponds. See Hobbs and Buckmaster article in Tideline (2011): 


Sidenote: The Thames.  A similar history of city growth, habitat loss, and sewage pollution then followed by gradual recovery has been experienced in many places around the globe. 


 2021: Upper Coyote Results. 

Summary of commonly caught critters.

  • Natives: Upper Coyote sloughs are #1 for native Longjaw Mudsuckers & Hemigrapsus (Oregon) Mud Crabs!  This area also had the second-highest numbers of native Anchovies, Starry Flounder, Bat Rays compared to all Lower South Bay segments monitored during Operation Guadalupe.
  • Non-Natives: Unfortunately, the Upper Coyote sloughs also support the most non-native Yellowfin Gobies, Inland Silversides, Corbula Clams & Harris Mud Crabs. The second-highest total of non-native Shimofuri Gobies was also tallied here.
  • No Leopard sharks and fewer Palaemon Shrimp were present owing to low salinity (fresher water) prevailing this far upstream.



Golden Anchovies at Art1 on 4 Sep.  Some of these fish are still browning down.

1843 Anchovies were counted in Upper Coyote, Dump, and Artesian Sloughs during the four trawling dates of Operation Guadalupe.  Most Anchovies in Upper Coyote Sloughs (1284 or 70 percent) were collected at upstream, fresher water stations.  Random ‘egg-checks’ invariably detected at least a few egg or milt-bearing Anchovies.

  • We suspect that Anchovies may be staging downstream where food is most available, then periodically running upstream for spawning.


Green Anchovy dorsal sides turn gold and brown in upstream sloughs.

Anchovies are members of the Clupeiform family of fishes. Four native Clupeiform fishes visit these upstream sloughs and marshes each year:  Northern Anchovies in summer and Pacific Herring, American Shad, and Threadfin Shad in winter.  All four species migrate upstream to these marshes and creeks for spawning.

  • The dorsal sides of all four appear blue to green in high salinity waters (above ~15 ppt). They all “brown down” to brown, gold, or translucent in lower salinity.
  • In Anchovies, the color change process may take as little as a few to several hours.


A blue-green and long-bodied adult at station Art2c on 4 September.

Blue and Green Anchovies.  A few large and vivid green or blue-backed Anchovies are nearly always found in the mix.  We continue to presume that these intense colors identify big adults that recently arrived from the ocean.  Blue slowly fades to green, then to gold and colorless as the Anchovy acclimates to fresher water.


Golden Anchovies, Art2 on 4 Sep.

Short, deeper-bodied Anchovy adults.  In addition to brown/clear dorsal sides, many Anchovies at upstream stations had short-deep bodies indicating growth in warmer estuarine waters (per Hubbs 1925).  It is not known whether year-round-resident Anchovies might make up a higher percentage of these upstream subpopulations compared to those farther downstream near stations Coy3 and Alv3.


Golden Anchovies at Art1 on 28 Aug.  These have longer skinnier bodies.  Did they grow up in cold seawater?

Anchovies are always most golden in Artesian Slough.  Constant exposure to freshwater effluent from the SJ-SC RWF causes these fish to “brown down” to their ultimate degree of clear/golden brownness.  Anchovies also turn golden at upstream UCoy and Dump slough stations, but the change is a little less consistent owing to salinity fluctuations at those locations.


Other Fishes.

Some examples of fresher water oriented fishes.  Natives on the left.  Non-natives on the right.

In all, 16 species of native and non-native fishes were caught in the upper Coyote area.  All of these tolerate marine or near-marine salinity levels, but they all have a strong preference for fresher water at least at some time during their life cycle, e.g. for spawning or recruiting. 

The warm and saltier summer season is usually characterized as “Anchovy and Goby season.”  Many other species that prefer either cooler or fresher water either flee the area or crowd upstream as the creeks and sloughs heat up and dry out.


Baby Bat Ray at Art2 on 4 September.

Bat Rays.  All 71 Bat Rays caught in Upper Coyote sloughs were babies.  All were caught at downstream stations in each slough.

Pregnant females migrate into Lower South Bay to give live birth to litters of 2 to 10 pups.  Bat Ray pups feed on mollusks and crustaceans in fresher water sloughs in relative safety from larger marine sharks.  The pups may impose significant control on non-native Corbula Clams in these sloughs.


Starry Flounder with Palaemon Shrimp. Art2, 4 Sep.

Starry Flounder.  Most of the 30 Starries were caught at UCoy stations. Though still small, they are reproductive.  They migrate up the main stem of Coyote Creek some unknown distance to find an appropriate spot for spawning. ( 


Mudsuckers at Art2 on 4 Sep.

Longjaw Mudsuckers.  89 Mudsuckers were netted mostly at upstream stations.  Mudsuckers live in marshy creeklets and can survive where there is practically no dissolved oxygen. They very likely compete against non-native Yellowfin and Tridentiger Gobies.  Non-native Stripped Bass almost certainly eat them.

  • Good News: Mudsucker numbers have increased a bit in the last few years.  We speculate that these natives were once more common in the main slough channels here.


Silverside explosion on 28 August at Art1

Inland Silversides.  Over 3600 non-native Silversides were found over the entire upper Coyote area.  The vast majority (3108) came from station Art1 alone.  Water at this station is consistently slightly warmer and much fresher than any other location.  

Silversides are very bad fish for this ecosystem!  They are notorious egg and larval fish eaters, and they reproduce rapidly when conditions are good for them.  They have largely replaced native fishes in many parts of California.

  • Silversides could pose a grave threat for native Anchovy and Longfin Smelt spawns.



Palaemon Shrimp in UCoy on 28 Aug.

Palaemon Shrimp (Palaemon macrodactylus).  Almost all shrimp caught during Operation Guadalupe were non-native Palaemon varieties.  As always, Palaemon Shrimp are more numerous at downstream stations in each creek or slough.  At least half of these shrimp were older females from last year. 

Older females from the previous year generate at least two broods of eggs during the warm season.  Young-of-year shrimp are slightly smaller and clear-bodied in this photo. Those that hatched in spring or early summer begin brooding their own eggs later the same summer. 


Exopalaemon Shrimp in Dump Slough.

Exopalaemon Shrimp (Palaemon modestus).  Exos are freshwater cousins of our regular Palaemon. 681 were counted in the Upper Coyote area.  Most of them were found at the upstream ends of Dump and Artesian Sloughs. 

  • Dump and Artesian Sloughs appear to serve as calm fresher water refuges for small pockets of Exos during this dry salty year. Roughly 200 and 400 shrimp were counted in Dump and Art respectively.  Most Exos were at upstream stations.
  • Only 56 Exos were seen in Upper Coyote slough itself. Most of those (47) were caught at station UCoy2, near the confluence with Dump Slough.

Crangon Shrimp.  ONLY ONE NATIVE CRANGON WAS CAUGHT IN THIS AREA!  We hope they return.  


Crabs and Clams. 

Hemigrapsus, aka “Oregon Mud Crab,” with friends.

Hemigrapsus Oregonensis (Oregon Mud Crab).  The upper Coyote area hosted the highest numbers of shore crabs. These small crabs tend to prefer turbid and brackish water where they feed on diatoms, green algae, and small invertebrates.  


Harris Mud Crab, Rhithropanopeus harrisii .  This crab is the non-native analog to the Hemi crab.  Harris Mud Crabs are East Coast natives that were introduced in California in 1937.  

  • During similar trawls in the 1980s, the Harris Crabs were the most common invertebrate caught at stations Coy2 and Coy3 just a little farther downstream. Now, they are fairly rare and almost restricted to this upstream area. 
  • Harris Crabs are not known to cause ecological harm here, but they are non-native.  


Non-native Corbula Clams (left) and two native Macoma (right).

Corbula Clams.  The Upper Coyote area was the Corbula Capital of Lower South Bay during Operation Guadalupe.  4324 clams were collected here: 1265 in Artesian Slough, 1101 in Dump slough, and 1958 at Upper Coyote (UCoy) stations.

  • Far more Corbula were found at downstream stations in these sloughs on every trawling date. In all other parts of our study area, Corbula tended to be more numerous upstream.   
  • These non-native clams are public enemy #1. Corbula out of control were a significant factor in destroying the Lower Delta/Suisun Bay ecosystem. It is likely that Bat Rays and Diving Ducks help prevent the same trophic disaster from happening here!   


Missing fishes. 

Always consider what you DON’T see:  A few formerly common native fishes are never seen nowadays.  


Summary of trawling catches – Upper Coyote sloughs.

Results by slough and date.

Salinity Gradient.  As always, most of the fish and bugs arrange themselves along the channels in response to salinity. Red triangles are used to highlight fish or bugs that were more numerous downstream. Green triangles illustrate when more of them were upstream.   

  • More Anchovies were consistently caught at upstream stations in Artesian and UCoy sloughs.  (In all other areas monitored during Operation Guadalupe, Anchovies showed either no trend or some preference for downstream stations.)  Could these upstream Anchovies be visiting spawners?  What percentage of local Anchovies spawn upstream?
  • American Shad. Only a few Shad were seen.  They return to the creeks each winter, so it is still very early to see them.  13 out of 15 were caught upstream at UCoy1. 
  • Shimofuri Gobies and Corbula Clams were consistently crowded at the downstream ends of all three sloughs. (Shimo and Corbula distribution in all LSB sloughs and creeks reflected a gradient that varied and probably reflected very specific salinity characteristics in each channel.)
  • As expected, Marine-oriented species, like Staghorn Sculpin, Starry Flounder, Bat Rays, and Palaemon Shrimp were most often caught at the downstream end of each of these sloughs. 


Overall results.

Slowly restoring habitats here support dozens of varieties of native and non-native aquatic macrofauna.


We are bound to others, past and present, and by each crime and every kindness we birth our future.”  David Mitchel.

Comments are closed.