Fish in the Bay – 9 April 2017 UC Davis Trawl – Longfin Smelt Spawn

I rode again with the UC Davis / Dr. Jim Hobbs fish monitoring survey on Sunday, April 9th.   For this email, I am sending more words and fewer pictures.  I realized mid-way through that the story is too big.  Pictures can wait.  The news is that Longfin Smelt are now confirmed as spawning in Lower South Bay – specifically in and around the restored salt ponds on Lower Coyote Creek.

First some context:  This year’s rains brought a tremendous amount of freshwater flushing throughout the Delta and San Francisco Bay.  Not the biggest flush in history, but it is the biggest I’ve seen since I started looking at this scientifically – probably the biggest flush since the 1998 El Nino.  Here in Lower South Bay (LSB) sloughs, salinity dropped from the normal teens to twenties (in parts per thousand (PPT)) down to less than 2 PPT as stormwater surged down Coyote Creek and Guadalupe River after early January.  Even at our station “SB03,” which is in LSB proper, salinity dropped from mid-to-high twenties down to around 5 ppt and has stayed there for over three months now.

Lower Coyote Creek became a freshwater lake:  Ryan Mayfield in our group built the above chart to show 2016-2017 salinity readings we take every two weeks.  The purple line shows flow measured at the USGS stream gauge station in Coyote Creek.

The salinity drop in sloughs was sharp and dramatic after December and correlates with the Coyote Creek flow surge.  By February, Jim Hobbs reported seeing dead clams and other benthic organisms that were likely signs of salinity shock in Lower Coyote Creek and Alviso Slough.

Close to where we work, near the San Jose-Santa Clara Regional Wastewater Facility, the Coyote Creek Bypass Channel got a rare workout.  This channel, on the south side of Newby Island, was constructed in the late-1980s to accommodate high flows out the lower portions of Coyote Creek.  I have seen flows through the bypass before, but never as high as seen in February.

Bypass channel full to the brim.  If you lived here and knew this area, you would appreciate how much land was underwater.  It stayed underwater for close to a week as flows continued to sluice down from the creek.  Essentially all Lower Coyote Creek turned into a freshwater lake, and so far, has remained largely fresh.

This once in a decade freshwater flush is very beneficial to ocean-going and estuarine fish that seek freshwaters to spawn.

The big news: Longfin Smelt larvae are found in Lower South Bay.  This is the first documentation that Longfin Smelt spawn in LSB.  Dr. Hobbs first reported longfin larvae in restored Pond A21 in March.  On April 8th and 9th, he found longfin larvae at several stations, including restored Ponds A19 and A21.  This is a huge Salt Pond Restoration Project success.  Longfins were listed as threatened by State of California in 2009. They are one of the pelagic fishes whose crashing populations characterize Pelagic Organism Decline (POD) in the Delta and North Bay.

Longfins have probably spawned around Lower Coyote Creek before, but no one ever documented it.  The UC Davis trawling effort since 2010, specifically looking for longfins, has never seen clear evidence of spawning until now.  We have seen adult longfins each winter … adult longfins ready to spawn … but, never larval fish, eggs, or other signs that spawning happened.    

Charts below show the effects of the freshwater flush as seen on April 8th and 9th.  At some stations, slough water was as fresh as tap water (less than 0.5 ppt). Water less than 2 ppt is often considered fresh enough for crop irrigation.  It is amazing to think that water at many of our sampling stations was so fresh it could be drinkable.

Map of trawl stations:

The freshwater flush of 2017 clearly stimulated the local longfin spawn event.  I focus on Longfin Smelt larva, but Prickly Sculpins and Sacramento Suckers are the other oddballs that we rarely or never see.   Young Herring are expected, but usually not so far downstream in Lower Coyote Creek.  This year was very wet and unusual for fish.


Dr. Hobbs and his team preserved larval longfins for otolith and diet studies.  This will reveal when and where these fish hatched, fed, and grew to current size and what they are eating. 

The Longfin spawn in LSB is a puzzle piece that Jim Hobbs spent years to find: Finally sweet SUCCESS!!  This has implications for the POD crisis in the Delta.  Now we know that Longfin spawning range is a little bigger.  Maybe there is more hope for preservation of this species in SF Bay.


The Delta Science Program under CALFED provides an overview of the POD issue at this link:

Unfortunately, of the four species that characterize POD, the Delta Smelt is on the brink of extinction.  Even more unfortunate, that fish does not tolerate salt water, so it will never transit and establish down in our southern area.  

But, you know what they say … three out of four ain’t bad!


Jim Ervin
Compliance Manager
San Jose-Santa Clara Regional Wastewater Facility


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