Fish in the Bay.  WRMP, Napa-Sonoma Wetlands Review – 2025.

This report is a brief “2025 Year-in-Review” for the Napa-Sonoma Marsh trawls.  Much of this is adapted from a webinar presentation I gave to the Napa-Sonoma Marshes Restoration Group Annual Meeting on December 10^th.

• The meeting was hosted via webinar by Loren Roman-Nunez from CDFW.  https://scc.ca.gov/napa-sonoma-marsh-restoration-group/ 

1. Background info.

As always, the boat, the crew, and the trawls are provided courtesy of the Otolith Geochemistry and Fish Ecology Lab (OGFL) under the direction of Dr. Levi Lewis.

• The few people you see on the boat are a metaphorical ‘tip of the iceberg.’ …

An additional small squad of people support the boat monitoring effort. They take care of boats and equipment, permitting, safety programs, maintenance, scheduling, data curation, and training in addition to performing all related lab work. They make our fish monitoring look fun and relatively effortless.

The OGFL team assesses these marshes through the use of “Otter Trawls.”  A net is dragged behind the boat at designated “stations” for five minutes.  Weighted “otter boards” on either side spread this particular net to roughly a 14ft width by 4 ft height. 

• As near as I have been able to tell, no one knows the exact origin of the name “otter trawl.”  It’s just a net system that has worked for 120+ years.
• From Google AI:  “The otter trawl, a highly efficient fishing net held open by angled “otter boards,” emerged in the late 19th century, evolving from earlier beam trawls and initially developed in Britain for recreational/scientific use before revolutionizing commercial fishing with steam-powered vessels in the 1890s, becoming a dominant method for harvesting bottom-dwelling fish and shrimp globally by the 20th century.” 

Where we trawl. 
Dr. Jim Hobbs initiated long-term monitoring of Lower South San Francisco Bay (LSB) in 2010.  At the time, the project was limited to studying native versus non-native fishes in restored salt ponds versus adjacent sloughs and creeks.

• Over time, the monitoring project expanded to evaluate threatened (now endangered) Longfin Smelt spawning habitat in LSB (funded by California Dept of Water Resources – DWR), and fishes and habitat affected by treated wastewater discharge (funded by the San Jose-Santa Clara Regional Wastewater Facility – SJ-SC RWF). 
• Starting in 2025, the WRMP provided additional funding to expand our trawling surveys into several new restored wetland “Operational Landscape Units” (OLUs) to the north: Bair Island and Eden Landing in South SF Bay, and Napa, Petaluma, Novato-Gallinas, and Wildcat marshes farther north in San Pablo Bay.
  • “An Operational Landscape Unit (OLU) is a connected geographic area sharing similar physical traits (like hydrology, geology, or land use) that benefit from being managed as a single unit for specific functions, often crossing traditional city/county lines to address ecosystem needs …”  https://www.wrmp.org/about/

The Napa – Sonoma OLU is a little wonky.  It stretches across of the north shore of San Pablo Bay.  The larger eastern “Napa” portion is dominated by flows from Napa River and Hudeman Slough.  The western “Sonoma” portion is largely fed by Tolay Creek and/or Petaluma River.

This long, seemingly “gerrymandered” OLU makes sense from bird and plant perspective, but from a fish or boat perspective, it is a little awkward.  As a practical matter, we trawl Sonoma Baylands on the same days that we trawl Petaluma River, and Sonoma raw data is recorded on Petaluma datasheets. It’s not important in the long run, but it does make subsequent data analysis and mapping a little more confusing and difficult.   

2.  Napa-Sonoma marshes as seen from the surface. 

For most folks who do not get out on the water, the best view of the Napa River and marsh system is from Highway 37, aka ‘the commute from Hell’ during rush hours.  This is the view of the bridge over the river with Mare Island in the far background. 
 

The view from the water is more delightful. 

Within each OLU there are different categories of restored or restoring sites that are evaluated over time: Benchmark, Reference, and Project sites.  Basically, …

• Benchmark sites were either never disturbed or were restored many decades to a century ago and are currently at environmental equilibrium.
• Reference sites are mature marshes that have attained a reasonable/achievable amount of restoration, something on the order of at least 20 years post restoration.
• Project sites are currently experiencing active or passive restoration.  Former salt ponds that were breached within the last 20-years or so fit this category.
• https://www.wrmp.org/wp-content/uploads/2023/04/Exec-Summary-and-Memo_WRMP-Priority-Monitoring-Site-Networks_20230419.pdf

The different categories of restoration sites are extremely important on the land for evaluation of vegetation cover and bird colonization.  For fish though, the age of the marsh is largely relevant only for the first few to several years of restoration. After tiny crustaceans and mollusks settle in, fish follow pretty quickly.  – At least that seems to be our experience in LSB.      

From the boat, we see a little of the different levels of plant succession and bird use of restored habitat.  Former salt ponds, Pond 2, and Pond 3 are filling in very nicely.  (These ponds were breached just over 20 years ago, but they may not have yet graduated to “Reference Site” status.)

However, more recently breached “Old Cargill Napa Plant” site and former Cullinan Ranch remain almost entirely subsided. Sedimentation and plant colonization need a few more years. (I did not include photos because there is nothing to see other than open water.)

3. Big Data.

This is a summary of 6 months of raw fish and bug data from the Napa OLU for the year. 

(Yes, this table is way too busy, and the font is far too small for formal presentation, but I presented it anyway. – Each number represents living creatures!  The second half of this presentation/blog post will focus on many of the more important ones.)

The table is divided into three parts highlighted in yellow for easy comparison of fish and bugs caught in each area over the same six months of trawling effort. 

• Top portion = Napa Marshes
• Middle portion = Sonoma Baylands + Dickson Unit (aka Sears Point)
• Bottom portion = Lower South Bay (LSB). 

Because LSB is sampled using 10-minute trawls versus 5-minute trawls for the other areas, the LSB raw numbers were divided by 2 to yield comparable “Catch Per Unit Effort (CPUE).  … An apples-to-apples comparison, so to speak.

 Results: Good = green.  Bad = red.  Ok = Yellow.

Green –

• Striped Bass. Bass counts at Napa are surprisingly high.  This is good news for sports anglers.  Maybe not such good news for Anchovies and Longfin Smelt.
• Tunicates and Dungeness Crabs.  Tunicates late in the year tell us that more microscopic productivity must be remaining in the system.  Dungeness Crabs are good crabs.  We like them.
• Longfin Smelt.  424 post larval Longfins were caught in April.  The CDFW Larval Smelt (SMS) Survey in Dec 2024 also caught 20,000+ larval longfins here!  Young Longfin are a huge sign of hope!
• Prickly Sculpin.  127 Pricklies from April through October.  We didn’t catch so many in any other “Operational Landscape Unit (OLU).  This is a good sign that the Napa tidal slough system is connected with upstream freshwater wetlands.  Prickleys are catadromous fishes.  They spawn in saline marshes and recruit in fresher upstream waters

Yellow(?) –

• Crangon shrimp. (Yellow)  Native Crangon shrimp numbers peaked in the summer.  It’s good that they are present.  It would be better if we saw many more of them.

Red –

• Only one Anchovy was seen in Napa Marshes in six months of trawling.  This is bitterly disappointing.  We caught many more Anchovies at the other SF Bay OLUs: Petaluma, Gallinas, Wildcat, Eden, Bair, and LSB.
• Corbula Clams and Musculista (Asian bag mussels) are invasive critters and generally bad signs. The numbers in Napa and Sonoma marshes were very low compared to LSB over the same months, but any Corbula is bad regardless of numbers. Corbula Clams are documented ecosystem killers in the SF Bay system. 

4. Biota.

4a. Fishes.

Trawls in April and May caught some of the most interesting native California fishes: Tule Perch, Sacramento Sucker, and Sacramento Splittail.  All three live all, or most, of their lives in freshwater creeks and rivers.  Not surprisingly, we caught most of them early in the year when waters were fresher.  Most were caught at fresher stations in the northern portion of our Napa trawling area.

Tule Perch count = 30 (April thru November). The map above shows the distribution of Tule Perch catches from six surveys in 2025.  Most Perch were found in Steamboat and Fagan Sloughs, several in Mud Slough, and a total of five at restoration site P2A2 in July and August.

Sacramento Sucker count = 1.  Of these three natives, the Sucker is the only one that still exists in our more familiar survey range in Lower South Bay (LSB). 

Tule Perch is a very special fish for us.  In roughly 15 years of surveying LSB, we have only caught two of these perches on separate occasions around 2019. In LSB, they were scrawny emaciated looking specimens, presumably some of the last survivors of a small population that may possibly still exist downstream of Anderson Dam on Coyote Creek.  These Napa River examples were the first healthy adult specimens I had ever seen.

• Like all surfperches, Tule Perch are live-bearing fishes. They do not lay eggs; adult females give live birth to 10 to 60 babies each year.
• The average lifespan of this fish is around 5 years.    
• I am told that males lose the light grey bars on their sides as they age.  However, this has not yet been confirmed.

Sacramento Splittail count = 14 in Napa, plus 4 in Sonoma Baylands.  Five Splittail were netted in April (including the four at Sonoma Baylands).  All the rest were caught in May.  As shown on the map, all Splittail were found at upstream stations of Steamboat and Mud Sloughs.

Splittail are members of the Cyprinid (minnow) family. They are a semi-anadromous fish that live in low-to-moderate salinity waters in summer.  They migrate upstream to fresher waters in winter through spring to spawn in floodplains.  Their spawning and recruitment success is highly dependent on rainwater flushing.  If the rivers don’t flow or the floodplains disappear from diking or development, Splittail populations diminish and eventually disappear.

Sacramento Splittail is another special fish for us.  According to literature, native Splittail were extirpated from Coyote Creek in LSB in 1980.  They have never been seen there since.

• Jim Hobbs taught me that there are two remaining populations of Splittail in the world: one primarily freshwater group in the Sacramento-San Joaquin river system as far downstream as Suisun Bay. The other population is in San Pablo Bay – primarily this Napa-Sonoma OLU system. The San Pablo Bay population is much more saltwater-tolerant.   
• If we are to ever repatriate Splittail to Coyote Creek in Santa Clara Valley, the new refugees would have to be sourced from this salt-tolerant San Pablo Bay population.
• We found only 18 Splittail in San Pablo Bay in 2025. This region has no Splittail to spare for foolish repatriation experiments at this time.  We must preserve this Napa-Sonoma population!   

Striped Bass count = 67, plus 15 in Sonoma Baylands (April thru November).  Stripers were caught in every month of sampling.  On a CPUE basis, this is more than double the number of Bass we saw in LSB over the same period.  This is because the mighty rivers of the Sacramento-San Joaquin delta are the major home-base for Stripers. LSB is a relatively minor cul-de-sac for these ‘brackish water barracudas.’

The fish we love to hate.  As game fish, Striped Bass are extremely important.  The vast majority of local anglers regularly seek to hook them, either for eating, or for catch-and-release.  But, as a conservation issue, this non-native fish is highly problematic. 

• We often wonder how many young Longfin Smelt, Tule Perch, or Sacramento Splittail might be in the belly of each Bass we catch.  However, our idle curiosity does not justify sacrifice of such mighty and desirable fish.  We release all Bass unharmed.    

Bass collage from Steamboat Slough in the later months of 2025.

Juvenile and young adult Striped Bass appear to congregate in Steamboat Slough.  (Curiously, very few were seen in adjacent Fagan Slough.)  These Bass represent just some of the predatory gauntlet through which thousands of larval Longfin Smelt, Anchovies, Herring, and other small migrating fishes must pass!

Longfin Smelt count = 67, plus 15 in Sonoma Baylands (April thru November). Longfin Smelt spawning and recruitment in Napa River is the most pressing concern at the moment.  This now endangered native was one of the most common fishes in SF Bay up until the 1980s. 

• 424 juvenile Longfins were caught in April.  The vast majority were seen at far upstream stations. 
• A few months earlier, larval smelt trawls by Calif. Department of Fish and Wildlife (CDFW) in December 2024 netted over 20,000 tiny thread-like larval Longfins near Steamboat Slough!    
• We now suspect a Longfin spawning ground may be just a short distance upstream on Napa River!

Longfin Smelt spawn in Bay creeks during the coldest months when winter rains freshen the waters. Hatchlings quickly migrate downstream and back out to sea by spring.  Summer heat can be deadly for them. Young-of-year and adults return to upstream marshes from October through December. 

• We caught only a glimmer of hope for the new year near the end of 2025: four young-of-year Longfins showed up at station P3-1 in November.  Perhaps many more spawning-ready adults were already stationing farther upstream for the winter spawn. 

Prickly Sculpin count = 127, none in Sonoma Baylands. Native Pricklys are an unusual example of a catadromous fish: adults migrate downstream to spawn.  Juveniles work their way back upsteam to grow and mature. They are a good indicator of a robust connection between downstream brackish marshes and upstream freshwater creeks. 

• The Prickly catch in Napa marshes was outstanding!  The comparable CPUE for LSB over the same period was only five! 
• At first we thought Pricklies must be migrating downstream from Hudeman and Napa Sloughs on the west side.  However, their numbers in Steamboat and Fagan Sloughs indicate that young Pricklies may be recruiting farther upstream in the main stem of Napa River.      

Shokihaze Goby count = 10, plus 15 in Sonoma Baylands. For better or worse, Shokihazes and other non-native gobies are here to stay.

• They say that the San Francisco Bay-Delta system is one of the most highly invaded estuaries in the world.  Gobies are just one category out of many non-native species that present an irreversible change from what Bay habitat was before all the major environmental disruptions of the past 150 years or so.
• How can we sustain healthy fin-fish production under such chaotic conditions?  If we don’t know, who does?       

Shimofuri Goby count = 64, plus 18 in Sonoma Baylands.  Non-native Shimos appear to compete head-to-head with Shokihazes but cause no apparent adverse impacts, other than pushing native Bay Gobies out of the region.

• As a small consolation, Shokehaze, Shimofuri, Chameleon, and Yellowfin Gobies are all much more attractive than the drab native Bay Gobies they seem to have replaced.  We might as well learn to appreciate these beautiful gobies. They are native now.     

Starry Flounder count = 23, plus 2 in Sonoma Baylands. The Starry count in Napa marshes is very encouraging.  It was close to double the CPUE count we saw in LSB over the same months!

• Napa marshes are a better spawning place for Starries compared to LSB.  

California Halibut count = 3, plus 2 in Sonoma Baylands.  The 5 Halibut in the Napa-Sonoma OLU in 2025 compares against 54 (CPUE) in LSB over the same months. 

• LSB is the better marsh for young Halibut recruitment!  The water is warmer, and there are more Anchovies and shrimp in the far southern corner of SF Bay.

4b. Invertebrates (Bugs). 

A general cavaet:  With the exception of shrimp and crabs, otter trawling is not an ideal method for surveying small invertebrates.  However, given constraints of time and budget, we still glean useful information about presence, absence, and relative abundance of smaller bugs. – We do the best we can with available resources!

4b(1). Crusty Bugs.

Crangon shrimp count = 2,381, plus 1,264 in Sonoma Baylands.  Shrimp numbers in the Napa-Sonoma system are good, but not yet great.  The comparable Crangon shrimp CPUE number in LSB was 7,756 over the same months.

• Shrimp are indicators of food abundance and also food sources for larger fishes like Striped Bass, Halibut, Sturgeon, and Staghorn Sculpin.
• It is encouraging to see native Crangon shrimp recruiting in the recently restored Napa marshes, but … the Napa system needs more shrimp!

Non-native shrimp counts in Napa-Sonoma combined: Palaemon ~400.  Exopalaemon ~ 75.  Comparable LSB numbers were roughly ten times greater.     

Dungeness Crab count = 18, plus one in Sonoma Baylands.  10 of these highly desirable native crabs were caught in Cullinan Ranch alone!  All were young, perhaps one to three years old(??). They were much too small for legal harvest. 

Harris Crab count = 84, plus one in Sonoma Baylands.  The comparable count of Harris crabs in LSB over the same months was one (1) single crab! 

• Harris Crabs are hardy scavengers and generally good indicators of recently (?) disturbed marshes.
  • Harris crab abundance in undisturbed Steamboat and Fagan Slough benchmark sites is a little puzzling.  It should suggest a minor disturbance somewhere nearby.

More Dungeness Crabs from the Cullinan Ranch restoration.
 
 

Tiny Bug counts: Thousands of Misids plus hundreds of Amphipods. Tiny bugs are excellent fish food.  Marshes cannot produce beautiful fishes if there is no food. 

• Mysids generally bloom in response to rainwater flushing.  We saw lots of Mysids early in the year and fewer of them after the rainy season. 
• More Mysids were caught in the relatively smaller Sonoma Baylands area compared to the much larger Napa marshes.  Mysids indicate that Sonoma Baylands is a very productive system
  • However, Amphipod counts were much higher in Napa.

Clams.  The otter trawl net is particularly un-optimized for clam collection, nonetheless, the limited clam information is useful. 

Non-native Corbula clams live on the surface of the muddy bottom, so otter trawls tend to pick them up fairly efficiently. Corbulas were regularly present at about half the Napa locations.  The largest concentrations were at stations P2A1 and Cul1.  Corbulas are very bad clams. 

Most other types of clams burrow deep in the mud far below the Otter net’s reach.  We occasionally found Macoma clams and a few Gemma Gemmas where the mud was soft and/or the clams were young.  A couple of handfuls of young Macomas were found in Cullinan Ranch (Cul1 and Cul2) in August and October. 

• Colonization by these filter-feeding clams is an essential element of ecological succession in the newer restored marshes.     

4b(2). Squishy Bugs.

Worms (segmented worms or Polychaetes) are very important for the marsh environment. They are excellent food for fishes and birds, and they till and condition the soil.  No garden should be without them.

• The otter net is very inefficient for collecting worms.  Nonetheless, we get clues about presence or absence. We count all worms, but we often encounter species we have not yet identified.  We do the best we can!   

Tunicate count – 2110, plus 5 in Sonoma Baylands.  Tunicates, aka Sea Grapes, are usually part of the end-of-year cleanup crew.  These filter-feeders bloom and grow big during the warmest months when phytoplankton density is high. (Tunicate populations can explode at other times of year, but late fall seems to be the most common time.)   

• All Tunicates in the Napa-Sonoma marshes were collected late in the year, October and November. 

Benthic Diatoms. An orange-brown sludge clogged the net when we trawled the downstream segments (Stations P2A1, Cul1 and Cul2) of Napa marshes in October and November. 

This “brown schmutz” is comprised of benthic diatoms that erupt during warm nutrient-rich conditions late in the year.  This is characteristic of primary succession in shallow marshes where filter-feeding invertebrates, like clams and worms, and vascular plants are still in short supply.  But, what do we know?  Life is a journey!   

5. People.

We hosted a few visitors during some of the Napa trawls.

Dr. Aviva Rossi.  A graduate of UC Santa Cruz with advanced degrees from University of San Francisco and UC Davis.  Aviva is the WRMP coordinator for the San Francisco Estuary Institute (SFEI). 

Dr. Amber Manfre. A UC Davis graduate and fifth generation Napa resident, and scientist.  Amber is currently one of five Supervisors for Napa County.  Amber serves on the Groundwater Sustainability Plan Advisory Committee and as Board Secretary for Protect Rural Napa, a local nonprofit.

Plus, one additional visitor in August. 

Christina Toms, PE.  Christina, the WRMP coordinator for the San Francisco Bay Regional Water Quality Control Board (Water Board) joined us in August.  For over 20 years, Christina has been studying the interface between applied science, engineering, and policy development to support ecosystem restoration. 

Fisherman John and Wesley, the Western Gull, greet us at Cuttings Wharf launch point on the Napa River every month.

• Fisherman John retired from his Mare Island job in the ship building industry some years ago.  He posts his own fish reports about his hook-and-line monitoring experiences almost daily on Facebook.  According to John, fish counts have been very low these last few months.  Cold weather and a long winter dry spell might be the reason.
• Wesley, the Western Gull.  Wesley suffered an injured wing sometime in early 2025 – the injury has since healed.  During recuperation, Wesley learned that life is easy at Cuttings Warf.  Anglers, like John, occasionally toss expired bait to Wesley.  Why would Wesley leave when food is abundant?  Other birds occasionally try to horn-in on Wesley’s action, but Wesley always wins! 
• We all wish we had such beautiful birds as our mascots!

Jane’s Addiction – Just Because