Fish in the Bay – December 2019, Special Report: Brown Shad after Bomb Cyclones & Atmospheric Rivers.

Hello again everyone.  If you live in the Bay Area you are aware that we had a lot of rain the first week of December.

Then we trawled Lower South Bay on December 7th and 8th as rain continued to fall.  It was a Shad paradise.  169 American Shad and 4 Threadfin Shad were caught and released.  (We caught only 5 Shad in November!)

Trawl map annotated with colorful Shad.

Freshwater was rushing out of the creeks and sloughs and flowing out (generally over) the salty Bay water as sampled our 20 stations.  … What did the rain bring?

  • Few fish before the rain! You may recall, we caught only 148 fish in our November trawls – before the rain.  Lowest weekend fish count ever!
  • More fish after. The December total fish count was 432. This was not a record by any means, but a substantial increase from dry times.  Fish need rain!
  • Brown Shad! In dry November, some American Shad were the bluest I ever saw.  FRESH WATER TURNED THEM BROWN!  Read on …


UC Davis boat being positioned for launch into Artesian Slough on December 8th.

Because the rains hit so hard the previous week, we experienced vast differences in salinity over our trawling area.  Waters were very fresh at the upstream ends of sloughs, down to 5 ppt or less, but still very salty farther out in the Bay, up to 29 ppt which is getting close to seawater salinity.

These were excellent conditions to test our Shad Color Hypothesis: Do Shad dorsal colors reliably change in response to salinity?  And if so, how much?


1. High Salinity = Blue Shad?

Two Longfin Smelt (top and right) & two American Shad (left and bottom) from Pond A21 on Saturday.

Freshwater from the rain had not yet penetrated Pond A21 on Saturday.  Pond salinity was still 23 ppt.  This is very high for this pond and the Shad were still very blue.

BTW: the big Longfin Smelt at top was the largest, and presumably the oldest, ever caught in UC Davis trawls (over 120mm).


As far as I know, these were the bluest Shad we have ever seen in Pond A21.

Background:  Shad and Longfin Smelt are pelagic fishes that typically return to Lower South Bay and Delta creeks in December.

Literature says:

  • American Shad are triggered by a change in sea temperature: In their East Coast homeland, a rise in temperature in the Atlantic calls adults back to their natal streams. I don’t know if the Pacific warms this time of year.  I don’t even know if Bay Area non-native shad go far out to sea here.  Most we caught are young, so they are not behaving like East Coast shad.  How did they know it was raining?  And, why do young shad return in December through March if not to spawn?


  • Longfin Smelt spawn in cold water, below 16 degrees C. Water temperatures fell below that threshold at some stations on 7 and 8 December.   But, it is still generally a little too early and warm.  We do not know exactly what triggers them to start staging.  Do they smell the rain?


American Shad in the Photarium.

I put some in the Photarium to capture their shimmering essence under different light angles.  This wasn’t very scientific, but it was pretty!

There were a few green and greenish-brown shad on the upstream side of Pond A21 (station A21-4).  Surface salinity dropped to 19.8 ppt at the end of that trawl.  This may indicate a blue-to-green inflection point at just below 20 ppt.


Salinity was highest in deep Lower South Bay (stations LSB1 & 2).  Shad were still blue but had a mottling of brownish patches.


I do not know why Shad show flashes of brown at highest salinity.  Did these Shad just swim in from fresher water?  Or, are they simply confused Shad.


Shad were again more uniformly blue at station Coy4 near the mouth of Lower Coyote Creek and Alviso Slough.  Salinity was 20 ppt.  Perhaps salinity in the range of 20 to 25 stimulates optimal blueness in this fish???  … More investigation needed!

Note: Shad dorsal colors to not appear to change in response to turbidity!  (See tables embedded in photo above.)  Intuitively, we would think that dorsal countershading ideally should match water color: blue in the blue and clear ocean; brown in turbid slough or creek water.  However, turbidity did not correlate with Shad color at all.  The highest overall turbidity was at station Coy4: 94 Nephlomatic Turbidity Units (NTU).   Nonetheless, Shad were blue!


2. Do Shad turn green below 20 ppt?

As we motored a short way up Lower Coyote Creek to station Coy3, salinity dropped below 20 ppt.  Shad turned green!


When we trawled Pond A19, further upstream, the following day, salinity was even lower.  Shad were green and shifting to brown.


Also note:  Threadfin Shad change color too!

Last month, I commented that Threadfins seem to always have the same lavendar-blue color.  I was wrong!  The four Threadfins caught the December weekend matched American Shad hues in all instances.


Station A19-4 is on the California Bulrush side of the Pond, so presumably, the location experiences fresher water on average.  Nonetheless, salinity was slightly higher at the time we trawled: 14 versus 13 ppt on the other side.  There was also a layer of very fresh water, less than 6 ppt, floating on the surface as we approached the Bay-side of the pond at the end of each trawl.  Shad were both green and brown!


The green-to-brown inflection point seems to be around 14 ppt.  How do our Shad change dorsal color so readily and reliably?


Station Art3 is just across Lower Coyote Creek from Pond A19.  Salinity was 2 to 3 ppt higher at 16.  Shad were again green and greenish-brown.


UC Davis Environmental Scientist, Jon Kuntz, examines three of the 17 Longfin Smelt caught on December 8th.


3. Brown Shad below 14 ppt?

We proceeded up Artesian Slough and watched salinity drop and Shad get browner.


Brown Shad closeup.  The Shad at center is a Threadfin.

Again, both American Shad and Threadfin Shad appear to experience the same color changes in response to salinity.


At the upper end of Artesian Slough, station Art1, the water was freshest and the Shad were fully brown.  This was more than a bronzy brown.  This was full-on chocolate-mahogany brown!

This station also has the lowest turbidity.  Like it or not, water originating from the San Jose-Santa Clara Regional Wastewater facility is very fresh, clean, and clear.  If shad changed color to match turbidity, they would be brightest blue here.


Alviso Slough.  It was the same story at almost all sloughs we sampled.   Upstream waters were fresher, and Shad were browner.


Upper Coyote Creek.  Single-digit salinity = brown shad.


Dump Slough was an interesting exception.  Salinity was low at the downstream end when we trawled … and Shad were brown.


4. Are Shad better than our instruments at detecting salinity?

Much to our surprise, we caught green shad at the upstream end of Dump Slough.  This made no sense until we looked at the salinity meter.  Salinity was 14 ppt.  It made perfect sense!  Shad do not lie!


A second and final surprise came when we trawled station Coy1 at the end of Sunday’s trawling.  This is well downstream from Pond A19, Artesian Slough, and Dump Slough.  We fully expected to see green shad at this station.

The Shad were brown!  Again, we checked the meter: salinity was in single digits, less than 6 on the surface at the end.  This was below the brown threshold for shad.


High tide was at 10:00 AM that day.  By 1:40 when we trawled at Coy1, a large pulse of fresh creek water had ebbed out this way.  The shad were again telling the truth.

As long as we catch Shad, we don’t need a salinity meter!


Allen Huynh, another Environmental Scientist with the UC Davis Otolith Geochemistry & Fish Ecology Lab, recorded water temperature, dissolved oxygen, salinity, and turbidity as we returned to base from our last trawl on Sunday.


5. Be the Aquaman! (or Aquaperson, if you prefer!)

Aquaman, courtesy of DC Comics and Warner Bros. Pictures

It makes me think …  One of Aquaman’s superpowers is his ability to communicate with the fish.  We just learned how to communicate salinity with our Shad.  Maybe we can catch up with Aquaman’s and Atlantean’s* superpowers   … one fish at a time.

* Aquaman comes to us from DC Comics:
Atlanteans are also superheroes from the Marvel Comic universe:  I take no position on which version displays greater fish telepathy powers.