Fish in the Bay – May 2025, WRMP San Pablo Bay Trawls, Part 2 – Petaluma River.

May 21, 2025 Jim Ervin
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Fieldwork, Fish in Lower South Bay, News

This is part 2 of a 4-part San Pablo Bay series. The UC Davis Otolith Geochemistry & Fish Ecology Lab (OGFL) was contracted via the Wetland Regional Monitoring Program (WRMP) to evaluate the underwater ecology of several restored wetlands around the shores of San Pablo Bay.  These are new territories for us. Who knows what we may find?   

We continue our journey around San Pablo Bay in a counterclockwise direction. 

  • Part 1: Napa River watershed – approximately 426 square miles (1,103 km²).
  • Part 2: Petaluma River watershed – 146 square miles (380 km2) + Novato Creek watershed – 45 square miles (120 km2). 
  • Part 3: Gallinas Creek watershed – 5.6 square miles + Miller Creek watershed – 12 square miles + Hamilton Wetlands Restoration Project.
  • Part 4: Wildcat Creek watershed – 11.1 square miles (29 km2) + San Pablo Creek watershed – 41 square miles.

Note for WRMP and restoration managers: Novato Creek is part of the Gallinas-Novato network of OLUs to the south.  Formally, Novato Creek results are reported under Gallinas-Novato OLU.  BUT for blog reporting, it makes more sense to report Novato fish and bug results with Petaluma. 

April results:

  • Many Mysids – excellent food for fishes.
  • 10 Baby Anchovies & 7 Baby Herring – at least some pelagic fishes recruit here; however, the Unidentified/Baby Goby count (11) was disappointingly low. 

May results:

  • Overall fish counts increased slightly partly due to a few more Unidentified/Baby Gobies, but the springtime Baby Goby total was still low in both April and May compared to Napa, Eden, and LSB surveys. 
  • Mysid count dropped by a third. Baby Anchovy & Herring counts dropped by almost half.
  • Striped Bass count doubled from 5 in April to 10 in May.

The remainder of this report is organized by creek or restoration segment.  However, fish and bug numbers discussed will generally be totals for the entire Petaluma system for each trawling day unless stated otherwise.  This is a little confusing.  –  growing pains as we learn these new restoration territories.  

1. Sonoma Baylands (Sob).

Sonoma Baylands is at the far western corner of a much larger “Sears Point Restoration Project.”  This 289-acre site was open to tidal flows in 1996.  In many ways, this site became the test-bed and prototype for the larger adjacent “Dickson Unit” restoration almost 20 years later.

The view in 2025: The new slough winds through fields of pickleweed and spartina.  Various types of shore birds congregate on the downstream shores near station Sob3.

History of Sonoma Baylands & the Dickson Unit restorations:

  • Bay Nature. Sears Point – 2007 https://baynature.org/article/sears-point/ 
    “In the early 1990s, accumulated knowledge was brought to bear on the site next to Sears Point called Sonoma Baylands. …  At 289 acres, the restoration site was larger than any yet treated. Like the typical diked field along San Pablo Bay, it had subsided several feet below sea level. …  In 1996, to great fanfare, Sonoma Baylands was reconnected to the estuary.”
  • Sears Point Restoration Project.  https://scc.ca.gov/climate-change/climate-ready-program/sears-point-restoration-project/
    “Slated for casino development, the 2,327-acre Sears Point property was acquired by Sonoma Land Trust in 2004. Diked and drained for over 120 years, the area had subsided 6 feet and was vulnerable to catastrophic flooding.
    In 2015, the Sonoma Land Trust and Ducks Unlimited breached the levee at two locations, reuniting tidal flow to 960 acres of the site …”
  • Sears Point trail offers new hiking spot near Petaluma – 2016.  https://www.petaluma360.com/article/news/sears-point-trail-offers-new-hiking-spot-near-petaluma/   
    “The Sonoma Land Trust purchased the property in 2005, as part of a $17 million arrangement …
    The newest addition, which the Refuge is calling the Dickson unit, adjoins the 300-acre Sonoma Baylands, opened up to salt water just over 20 years ago but well on its way to full recovery.”
  • Greening Dickson’s Heights – 2018 https://archive.estuarynews.org/estuary-news-dickson-mounds-erosion-research/  “Looking east from the levee-top trail, a silvery swath of bay is dotted with low islands — some tufted with plants, others mere muddy humps that barely break the surface. … 
    The islands, 500 in all, are actually man-made mounds, scattered across the mudflat as an integral part of the restoration design.”

Big Fishes at Petaluma stations. 

  • Sacramento Splittail count = 4 in April, 0 in May.  These were the total April/May Splittail counts for Petaluma + Novato Creek.   
  • California Halibut count = 2 in April, 0 in May.  Again, the Halibut shown above, at station Sob3, were the only two caught in Petaluma + Novato Creek for April/May.
  • Striped Bass count = 5 in April, 10 in May.  This result was a little more encouraging, if you like Striped Bass.  The Bass number (from all stations combined) doubled from April to May. 

Tiny Fishes and Bugs.

  • Staghorn Sculpin count = 16 in April, 18 in May.  Young Staghorns recruit here.  We caught them mostly at Sob stations in April, then exclusively farther upstream at Bah stations in May. 
  • Northern Anchovy count = 10 in April, 6 in May.  Anchovies also recruit here, albeit in low numbers compared to what we see in other parts of SF Bay.  No adult anchovies have been seen so far. 
  • Longfin count = 1.  A single baby Longfin was caught at station Sob3 in April.  Preliminary speculation: This baby might have been blown in from restored Napa-Sonoma marshes to the west. 
  • Crangon shrimp count = 738 in April, 430 in May.  Good News!  Young Crangon were present at most stations, especially in the downstream ends of main channels.  Non-native Palaemon and Exopalaemon shrimp catches were much lower.
  • Mysid count = 6142 in April, 1844 in May.  Mysids are midget-sized shrimp-like crustaceans. They are essential food for small fishes.

2. Black John Slough (BJS).

Black John Slough (BJS1), 21 May.

Black John Slough is a northern connection between Petaluma River and the Bahia Marsh and Rush Creek restorations. 

  • Marin County Flood Control District.  Rush Creek land use and habitat https://flooddistrict.marincounty.gov/rush-creek-land-use-and-habitat/   “Northeastern Novato stormwater flows into two places. The first is Rush Creek, which then flows into Black John Slough and to the Petaluma River. The second place is the Deer Island Basin and Simmons Slough. Simmons Slough goes to Novato Creek by pump.”

Fish catches at Black John Slough were sparse.  Three Shokihaze Gobies and one American Shad in April, and five gobies, two sculpins, and a Stickleback in May. 

Invertebrate counts were a little more interesting: 

  • Zero Harris Crabs out of 5 for all Petaluma stations in April, and 15 Harris Crabs in May – with only three more caught immediately downstream at station Bah1. 
  • 230 Palaemon shrimp were caught at BJS1 in May out of 243 total.  In April, the BJS1 Palaemon catch was an unexceptional 19 out of 88. 
  • 100 Macoma clams and 200 Corbula clams were picked up at BJS1 in May.  The datasheet notes that this was a difficult slough.  Two trawls had to be aborted due to giant mudballs.  The high number of benthic invertebrates was no doubt influenced by the rough and muddy bottom.

3. Bahia Marsh (Bah).

Bahia Marsh stations, Bah1 & 2, are at the downstream end of the southern slough that drains the Bahia Marsh restoration area.  Station Bah3 is in the main channel of Petaluma river immediately downstream.

  • SFEP – Bahia Marsh Restoration   “Bahia Marsh is a 632 acre tidally influenced wetland in Novato (Marin County) tucked just inside the mouth of the Petaluma River.”
     https://archive.estuarynews.org/1-white-board-1/ 
  • From litigation to renovation: Novato’s Bahia neighborhood is reborn – 2019  https://www.marinij.com/2014/06/22/from-litigation-to-renovation-novatos-bahia-neighborhood-is-reborn/ 
    “After a 1987 dredging, over time the lagoon began to fill with silt. Plans to dredge were met with opposition from public agencies and environmental groups. Residents became embroiled in a lengthy and expensive legal battle. Some wanted the dredging, others did not want to bear the expense.
    A developer offered to pay for the dredging as part of a proposed 424-home development planned for Bahia. However, though the City Council approved the developer’s project, opposition from critics killed the plan, Thompson said. The developer eventually sold the land to the Audubon Society.”
  • Bahia – 10 Years Later (2019) https://marinaudubon.org/pdf/TheRail_Jan2019_Web.pdf 
    “In the 2008 restoration, tidal action was restored to 139 acres in Central Bahia by breaching levees and excavating channels within the new marsh plain. In 2013, additional breaches were made in the levee connecting Black John Slough to the 216-acre West Bahia. Prior to that, several breaches occurred naturally in the levee between Central and West Bahia.”

More painful history of litigation is summarized here.

  • Starry Flounder count = zero in April, four in May.  All four baby Starries in May were caught at stations Bah2 and Bah3.   Those stations are in, or immediately adjacent to the main stem of the Petaluma River.  Starries generally prefer deeper river and creek channels.
  • Bay Pipefish count = 1 in April, and 1 in May.  Pipefish tend to hide amongst marsh plants near the shoreline.  The two we caught here, one at Bah1 in May and one at Nov2 in April, are just indicators that more Pipefish are probably present in the weeds.
  • Ribbed Horse Mussel count = 1.  Otter trawls catch these mussels on rare occasion.  They cling tightly to roots and rhizomes of marsh plants, so it is very uncommon to catch a live one in an otter trawl.  They are non-native but generally beneficial.
    • Ribbed Horse Mussel (Geukensia demissa) https://en.wikipedia.org/wiki/Geukensia_demissa
      • The ribbed mussel is primarily a filter feeder, and they help to clean said area of bacteria, parasites, and heavy metals.They feed on phytoplankton, bacteria, and non-flagellates to gain nutrients.
      • … mussels contribute bioavailable nitrogen in their pseudofeces. When ribbed mussels form mussel mounds, they are able to stabilize the ground to make it easier for Spartina to grow on.[17]

Brown Rockfish count = 3.  This was our most interesting catch by far.  We have only ever seen baby Brown Rockfish on two or three occasions in LSB.  They are long-lived bottom fishes in deep coastal waters.  A 25-year lifespan is typical, some live much longer!  These little ones were picked up at station Bah3 in the middle of the Petaluma River channel.  Salinity was around 15.5 ppt, not the marine-level salinity (~33ppt) where we would normally expect to find them.  It will be very exciting if we find them again in future trawls.

  • Brown Rockfish per Wikipedia. https://en.wikipedia.org/wiki/Brown_rockfish 
    “The brown rockfish has a long pelagic juvenile stage which spends two and a half to three months in the water column before they settle in shallow water to depths of 36 m (118 ft). This settlement can take place as early as May and the juveniles and subadults are common close to the bottom in bays and estuaries. In some areas, like San Francisco Bay …

    The brown rockfish was common in fish markets near San Francisco in the 19th century, as they are caught in bays and other shallow waters. Modern commercial fisheries regard this species as of moderate importance in fisheries for fresh fish and of greater importance in fisheries for live fish. Artisanal fisheries take this species on Baja California. It is an important quarry species for recreational fishers from Puget Sound south to northern Baja.”

4. Novato Creek (Nov).

We trawl only the far downstream end of Novato Creek.  This part of the creek is tidally influenced.  Salinity was in the mid-teens in April.  By May, salinity at all three Nov stations had risen to between ~19 to 21 ppt. 

  • Your Novato Creek Watershed.  https://www.streetstocreeks.org/novato-creek-watershed/ 
    “The Novato Creek Watershed is a 48 square mile basin and is the largest watershed in eastern Marin County. Its creeks flow through unincorporated Marin County and the City of Novato before crossing under Hwy 101, spreading out into tidal wetlands as it crosses under Hwy 37 and winds around Bel Marin Keys on its way out to San Pablo Bay near the mouth of the Petaluma River.
  • Marin County Flood Control District – Novato Creek land use and habitat https://flooddistrict.marincounty.gov/novato-creek-land-use-and-habitat/
    “Land protection and restoration efforts in the watershed include:
    • Hamilton Wetland Restoration project
    • Rush Creek restoration project
    • Bahia restoration project”
  • Striped Bass, Staghorn Sculpin, baby Anchovies, and some baby gobies were present in lower Novato Creek. 
  • Pacific Herring count = 7 in April, 3 in May.  Only one baby Herring was caught at Nov1 in each month, but we found this clump of eggs at the same location in May.  It is still very early to tell, but Novato Creek could be, and should be, a Herring hatching and recruitment place. 
  • Macoma clam count = 23 in April, 105 in May.  Native Macoma clams live deep in the mud. We rarely see them.  As noted above, the 100 individuals caught at BJS1 were probably from an accidental mudball. 
  • Corbula Clam count = 758 in April, 417 in May.  Corbula were present at all stations in the Petaluma area in April and May except Sob1, Sob2, and Bah1. 
  • High numbers of Corbula (121-325) were seen at stations Nov1 and BJS1 in both months.  However, these numbers pale in comparison to the thousands caught in LSB in each of the same months.   

Striped Bass know where the food is!

Bonus worms. 

Polychaete count = 6 in April, 1 in May.  Polychaete worms live deep in the mud.  We only catch them occasionally. 

  • This variety of Nereid Polychaete, a.k.a. “Pile Worm,” is non-native but still extremely beneficial.  He/She plows the soil like the distant cousin, the Earthworm.  This worm provides excellent food for any fish or bird smart enough to catch him.
  • Warning:  Pile worms have a pair of sharp mandibles deep inside the esophagus.  It is not their primary defensive weapon, and they usually don’t display these “fangs.”  But, exercise caution.  Bait collectors on the East Coast tell us that some species do bite, and it stings like a bee!  
  • Treat them with respect.  We have handled, and released, many of these worms in SF Bay.  We have never been bitten.  

Fieldwork, Fish in Lower South Bay, News
Fieldwork, Fish in Lower South Bay, News