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Smolt Monitoring in Marin County

April 8 2017

My name is Neely and I am a field scientist in training. Here I will document a fisheries field study and hopefully inspire some ocean stewards along the way.

About 1 in 5 of the homeric-journeying central coast California salmonids are born and die in the Lagunitas Creek Watershed in Marin County. Unfortunately this fish population is estimated to be down to about 8% of it's historic size. Salmon Protection and Watershed Network (SPAWN) works with county and state agencies to count, monitor and evaluate the state of the population and best practices to save our fishy friends (aka keystone species).

April 8 2017


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Debriefing Stage

And that's a wrap!

Bon voyage from a Coho born this Spring 2017.

SPAWN spent its Spring mornings counting juvenile salmonids swimming to sea for the first time (smolts) because this life stage will be a make-or-break point for the year class. Decades of research have proven salmonid populations are about as successful as their smolt life stage is in freshwater.

A healthy aquatic ecosystem will produce fat, healthy smolt populations expressing a full range of the phenotypes and adaptations in that gene pool. Smolt monitoring tracks how fat, healthy and abundant an out-migrating salmonid population is. A population with a full arsenal of adaptability has the capacity to respond and survive environmental changes like temperature fluctuations and precipitation variability. If a wild stock of salmon, such as the juveniles we counted this Spring, is able to maintain it's full range of diversity and genetic variations, it will retain the capacity to adapt.

Neely! This was such an awesome field season to follow along with. I feel like we all learned so much from your detailed analysis and reporting. Well done!

Mission Underway

2017 Population Estimate for Outmigrating Coho Smolts: 1,097 (+/- 184)

Comparison of this year's DARR (Darroch Analysis with Rank Reduction) results to past mark recapture data is pictured. More information about the software and it's uses can be found at the source .

Smolt Monitoring yearly results are acquired by organizing the number of new mark IDs throughout the weeks of the study in a pivot table and uploading the pivot table in a specific format into R. The DARR program is written by NOAA SW Fisheries and is a standard software used in fisheries population studies.

The goal of this study was to estimate the productivity of the salmonid population in their freshwater habitat. Smolt abundance can indicate the fitness of the spawning adult population and can offer insightful data for evaluating the viability of a depleted population.

That being said, when I look at this population estimate compared to past years, I think I initially see the major California drought from 2008 to 2014 and I think I can see the major El Nino events that warmed the Pacific and starved off salmon populations.

Outside viewers might see a fish species that survives through the most extreme droughts and severe rainfall. Someone might see a population recovery this year for this year class (this 2017 group was last seen in 2014, 2011 and 2008).

As long as a year class of baby salmon is able to fully express itself--meaning majority of young of the year survive- the population possess the ability to adapt. Some of those small fish will be great at thriving in warmer, low flow waters and some will be better at dodging orcas and surviving high flow seasons. The population contains the genetic diversity it needs to adapt to large environmental changes.

When I look at this graph, I also see an advocacy organization that has not consistently collected or maintained its data for the past eleven years and makes it hard for me to draw any definitive conclusions or attempt to publish.

It has been a journey running this project and learning the ins and outs of what it takes to manage a field site. SPAWN itself is still in the learning stages.

I want to reiterate what I said at the beginning of this field journal: it is crucial for non-profits, the government and citizen scientists to work together. I had to advocate for weeks for the minimum number of bubblers to safely run this project and sometimes the trap was almost pulled out of the water because no one else on the permits would make themselves available for a few hours some mornings. I would not have been successful in this project without the help and time and smiles of my weekly citizen scientists and the county fisheries biologists working farther down the watershed keeping an eye out. Species circling extinction, like Coho Salmon in California, will be saved by informed, unified efforts.

I hope this little salmon research project offers any future readers insight into fisheries biologist and an unbiased, science-based glimpse at the status of the watershed.

Swim on!

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  • 2017 Smolt Monitoring In Marin County: *

Summary of the Study Results

  • 576 smolt captures
  • 566 Coho
  • 10 Steelhead (SH)

Re-capture rate: 47% (this is great)

Average Coho:

  • Weight: 12.84 g
  • Fork Length: 104.93 mm

FRY: 1621 total

  • 1368 SH Fry
  • 253 Coho

Highest Catch: Week of 4/24-4/30 : 488 Fry : 292 Coho. 170 New/ 122 Recaptures

Pictured: *Mark ID re-captures by week looks at the return clips researchers counted on fish versus the overall population counted.

  • Researchers counting smolts back in April.
  • The daily set-up on San Geronimo Creek
  • Coho and Steelhead parr who will smolt in a year when longer hours of daylight will cue their thyroid to stop depositing the melanin parr bars and they will begin turning a distinctive silvery color.

Compared to past years, 2017 smolts were physiologically average and healthy. Less smolts were counted this year and this is most likely due to a large rain event mid-April that pulsed many smolts down the creek. Next year's numbers will tell researchers how the redds and young of the year fared in this year's unusually crazy Winter rain events. A salmon council meeting will meet at the end of June to compare numbers and published report on California Coho Salmon will be produced by NOAA's Southwest Fisheries center.

DARR analysis to follow, using the Mark ID proportions, as a final post with an estimation of the total population we measured swimming by this year.

Swim on!

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May Summary

As fish nerds exited the creek on May 23rd, flows were down to 3 cfs (this is a lazy, sluggish, summer creek speed).

169 Coho were captured in the month of May. This brings the study total to 566 Coho captures. 10 Steelhead were seen throughout the study, with only 2 showing up in May. (Steelhead and Coho presence on the watershed is an inverse relationship).

*May Averages *

*Water temp: 13.5 *Average Coho Weight: 12.28 g *Average Coho Length: 104.36 mm


2017 weekly smolt counts are congruent with historical data that shows the largest push of out-migrating smolts is the last week of April.

Pictured is about what 2017 final tallies will look like. Year to year comparisons to follow-up in the wrap-up.


09:30: *PVC Pipe found disconnected from live trap this morning. *

Couple handfuls of debris and a couple of parr were present in trap.

* Potential causes: *

  1. George, the resident deer, being clumsy as he crosses the creek.
  2. PVC joint had been sitting loose and large clump of debris may have jostled it free.
  3. The downstream landowner (he's a grumpy, anti-science individual) was being vindictive -- although this is highly unlikely.

Oh well! On the upside--it's the end of the season and there would not have been many smolts to count. On the downside, there is no down side. When we start getting one or less smolts a day for three days in a row, it's time to close the season.

They grow up so fast!

Q: Why are the freshwater fish less elusive?

A: I haven't been able to find a specific answer for why the freshwater natives are easier to catch. It seems that sometimes we catch the salmon fry by luck in the hand net and scoop out the California roaches with more ease.

Is this because of the species different life strategies? Or Intelligence? Or Fitness of the lineage?

My first thought was prey selection-which is well-established influence of selection. But the California roaches and salmonids look almost identical from the top and occupy the same freshwater habitat. So that might not be a solid answer.

I'm not well-versed on fish intelligence. Almost all fish are visual predators so it's hard to say for sure that salmon can see a net better than a native freshwater fish in the same water.

The final idea-- Almost 90% of all salmonid fry (everywhere) are going to either get eaten or die from disease or starve. The lineage of fish in this watershed have most recently survived ten years of drought and two El Nino events. So I would guess the stakes haven't been as high for the native freshwater fish (again, I don't have scientific studies backing up this idea) so they haven't evolved to be as fast or nimble.

It's an interesting question!

Glad you're still following this thread! Thanks for catching us up on your questioning.

I try to check in! Thanks for asking questions!

Salmonid Fry Growth

It used to take a good hour to chase down all the zippy little fry in our live trap box. They were about an inch long in mid-April.

A month later, it still takes a good hour to chase down all the zippy little fry in our live trap box because they are twice as large! No, it's not the exact same fish we're catching, but it is the same age group. I started taking extra notes to document fry growth because I felt like each week they went up a size class (You can check out what actually happened on the graph).

Salmonids come out of their nests in early Spring and will feast on whatever they can catch and fits in their mouth. In the beginning stages of life, this range is limited to small zooplankton. Eventually, they are fast enough to fit large zooplankton and will continue to eat their way up the freshwater food chain until their smolts.

The Steelhead young of the year we're seeing have graduated to eating bugs right when the first Spring insects are coming out in mass. The effect of added protein in a fry diet is reflective of adult salmonids gaining access to ocean nutrients and gaining anywhere from ten to thirty pounds in a year. Pretty amazing!

  • Pictured is a 30-35mm California roach (I didn't have a small Steelhead to compare that day) next to 55-60mm Steelhead fry. *
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Field Journal Musings:

  • [ ] Does today's colder water actually make the fish more active? Like are they really breathing more oxygenated water or are my hands numb so they seem more wiggly?

  • [ ] Do they fish notice the color morphs on each other? Note to self: look up past research on smolt color variations

  • [ ] Research has come out confirming fish talk to one the recaptures tell the others about the net downstream? Can they hear each other screaming as I process them?

  • [ ] Coho parr are definitely smarter than the fresh water fish. It's easy to catch a California Roach. Coho literally dodge and weave the net.

Pictured is my co-worker Elizabeth, contemplating fish.


It's so much fun to read these updates! I'm curious about the smolt color variations, too!

Agree with Margaret! Very fun and enlightening to follow. Why do you think the fresh water fish are less elusive?

Today we counted 17 Coho smolts en route to Tomales Bay.

When I explain the life of a coho salmon to visitors at our trap, I liken the Coho's time in Lagunitas Watershed to years a kid spends in school. San Geronimo Creek is like elementary and middle school to Coho. The fish are slowly gaining a more adventurous diet (moving from tiny zooplankton to small insects) and they are growing very quickly. Lagunitas Creek is where a Coho spends it high school years in faster currents eating a full bug (protein!) diet. Finally, the time spend in the estuary, Tomales Bay, is like college. Coho undergo physiological changes from fresh to saltwater fish. At the end, it's like graduating from the eccentric but consistent college cafeteria into adult land--the Ocean!

Fish Eye View:

Awkward video of some steelhead fry in a jar. I lowered the camera into the jar to see if the view would be any more interesting (nope).

I want to talk about the bubbler that makes a brief cameo at the end.

Bubblers= aerators. They add oxygen to an aquatic environment.

What happens when a fish is in a small, enclosed environment, like a bucket, is they run out of oxygen.

Bubbles 101

Basic understanding of how fish breathe: Oxygen dissolved in water goes into a fish and out comes carbon dioxide. The CO2 is absorbs into the surrounding water and eventually dissipates into the atmosphere through aeration (bubbles!) An air bubble rising through water is simultaneously dissolving oxygen into the water and absorbing CO2 as it reaches the surface. A bubble popping at the surface is releasing CO2 into the atmosphere.

When aerators are on, they will try to keep oxygen levels at normal conditions.In a stream or creek, a lot more processes are at work incorporating dissolved oxygen into the ecosystem. In our case, leaving a ton of fish in a bucket of still water is risky! Adding a bubbler allows fish to breath normally while they are processed for the study.

In summary, an aerator is to a fish what a snorkel is to humans: a consist supply of breathable oxygen.


The many color morphs of California Coho Smolts!

Is it ...Diet? Genetics? The color of the bucket?

  • Pictured: *

  • Brown

  • Green

  • Blackish (actually that dark, not just the shadow!)

  • Silvery (A fully smolted Coho with no parr marks left. I like to think of these guys as the fish who have stopped eating and are dead set on swimming towards salt water).

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April Update!

Averages for the month:

  • Stream temperature: 12 C

  • Air Temperature: 22 C

  • Max stream flow: 1,032 cfs

  • Min stream flow: 8.67 cfs

  • Average coho weight: 105.4 g

  • Average coho length: 114.5 mm

* Total Salmonid takes: 397 *

  • --Coho: 252
  • --Steelhead: 10

"Take" defined by the Endangered Species Act means to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to engage in any such conduct. 397 times a fish was captured in our net in April, although only 262 new salmonids were counted. The other 145 account for recapture counts.

At this time last year, 334 coho smolts had been counted swimming to sea. This year we have only counted 252 coho smolts. We suspect that the 5 inches of rain early in the month kept us out of the creek and helped a lot of fish make a break for it.

Swim on!


When taking measurements, I call out the data to my volunteer scribe.

Fish we have never caught before are recorded as "New (N)" and I give them a fin clip. These fish go in the upstream bucket to mix with the greater out-migrating population of smolts. Pictured is a coho in a tray of water where it has just been measured and given an upper caudal clip.

My volunteers and coworkers kindly tolerate me talking to the fish. I imagine it's like going to the doctor as a kid and you make it through getting weighed and prodded, and then the doctor announces you're getting a shot...just a really rude surprise. So I know the words are meaningless but I try to gently talk the fish through the clip anyway.

Fish we re-capture, as marked by a fin clip, are recorded as "R" and moved to the downstream bucket. These fish will continue on their way to sea, down stream of the trap.

For each fish, the whole measuring process takes about 30 seconds.

In the second picture, I have walked a recently marked bucket of new salmonids up the creek. Instead of pouring the fish out, I gently tilt the bucket sideways so they can swim out. And I always say, "Good luck!"

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Fish are not all a fyke net catches!
In the live trap this past week, researchers have found:

  • blue gill
  • golden roach
  • three spine stickleback
  • crawdads
  • bull frog
  • giant pacific newt

For personal interest in understanding the Lagunitas Watershed, SPAWN measures, weighs and photographs all species in case the data is useful for another project.


Interesting! How do you make them available? Do you upload these to iNaturalist?

Hey, we do not although that's a great idea. We take the picture on a water proof camera and store them with correlating information.

Preston up to bat processing fish. Biologists rotate every 10 fish for accuracy and cold fingers.
Preston will call out: species, fork length (mm), weight (g), fish condition, if a PIT tag is present, what the mark ID is/if present, and whether it's a new or recapture and the corresponding photo number. I record this info when I'm not puttering around on OpenExplorer. Woo!


Mark Recapture Method

Fun Fact: The first recorded mark recapture study was conducted on the population of London in 1629. If anyone knows how this guy was marking people...please let me know.

There are * 4 Assumptions * this method operates under:

  1. The population is closed. During the study, there are no deaths, births, immigration or emigration within the population in question. In order to ensure accuracy, it is assumed that during the study nothing is happening to disrupt the proportion of marked to unmarked fish.
  2. There is constant, equal chance for all individuals, marked or unmarked, to be caught during the study.
  3. There is time for marked individuals to randomly re-disperse into the greater population following each capture.
  4. Animals do not lose their marks.

The Mark Recapture Method answers a simple question: how many fish are in this population?

The principle: If a proportion of the population is marked, returns to the original population and then, after complete mixing, a second sample is taken, the proportion of marked individuals in the second sample will be the same as was marked initially in the total population.

R (marked recaptures) / T (total in second sample) = M (marked initially) / N (total population size)


N = (M *T ) / R

In these mark recapture studies, salmonids are marked with fin clips. A clip means a few fin rays are distinctively snipped. Salmonids normally accrue rips and tears on their fins so often fin clip schedules will include a small clip from two different fins. Markings are predetermined to correspond to calendar weeks. All participating agencies on the Lagunitas Watershed follow a coordinated fin clip schedule.

At the end of the smolt monitoring season, counts on how many fish were marked initially are compared to the total number of marked fish that were recaptured using R.

Past studies conducted by SPAWN and the Marin Municipal Watershed District (MMWD) have shown that the San Geronimo Creek Watershed, within the greater Lagunitas Watershed, contributes up to 50% of smolt production even though it accounts for only 10% of the watershed size.

Updates to follow on how counts are going and answers to follow on the ubiquitous "So, how are the salmon doing?"


This is really great! Thanks for sharing the method and formula Neely. Also, great diagram!

The Big Red Cooler

Every morning this Spring there is a chance to catch smolts out migrating to the estuary. There is also a chance to catch a couple of wader-clad, caffeinated fish nerds hauling their red cooler of gear down to the creek.

This big red cooler holds all our precious fish monitoring equipment.

  • Biomark reader
  • Clipboard + data sheets + pencils
  • Thermometer
  • Measuring tray
  • A scale that trial and error taught us to keep in a gallon bag. (Is anything electronic truly waterproof?)
  • Alka-seltzer tablets
  • Scissors + small bottle of alcohol to disinfect scissors between each use
  • Waterproof camera

Every smolt gets measured, weighed, fin-clipped, photographed and checked for a pit tag.

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Preparation Stage

Mission Underway:

Smolt Monitoring 2017 is GO!


Excited to hear how everything is going! A question just came up about this on Twitter: Are smolt any young fish or salmon and steelhead trout in particular? Thank you!

Saturday April 15th SPAWN Biologists trained some fishy citizen scientists!

Pictured is the day to day set-up including the fancy bucket a biologist sits on while we take smolt measurements.

Due to the ESA (Endangered Species Act), only those listed on federal research permits are allowed to actually handle the fish. SPAWN volunteers are crucial in efficient collection of data! Shown below is Preston demonstrating to a group how to tare the scale, and measure a fish.

My favorite picture of the day was Ken smiling as he held a jar we put a coho and steelhead fry in for quick comparison of characteristics. Ken normally works as a lab version of a researcher and is giving a day a week to work as a field researcher with us. You rock dude!

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Watson and Creek (are those guys too villainized to joke about now?) are all smiles because the trap is set-up and it's finally beer o-clock.

Ready for our volunteers training in the morning!


SPAWN's fyke trap consists of:

  • a 9 x 4 ft bag net
  • two wing walls (wooden frames covered with hardware cloth)
  • three ropes
  • three PVC pipes
  • six t-posts
  • a live trap (pvc box covered in mesh).

It takes about five hours to set up!

Picture below are the before and after photos of 2017 Fyke Trap: Round 2.

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Brave smile by our head biologist before climbing into a cold-water creek to set the trap up.

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Adding to the random field biologist skill-set: sewing!

12:00 * Getting ready to set our trusty, weather-beaten fyke trap back up this afternoon.*

Never thought I'd be spending afternoons sitting in a redwood grove with a one inch needle and reel of fishing line mending a net.

SPAWN is stoked to train our Citizen Scientists tomorrow morning on salmonid ID and monitoring protocol. We're a ambitious non-profit, but SPAWN is small. And we couldn't efficiently collect the quality and amount of data we get every year without the help of our dedicated, weekly volunteers.


Wish I could make it tomorrow! Next time!

Trials and Tribulations of Fish Monitoring

    1. Really cold water
    1. Pretty quick current
    1. Distracting, adorable school of Coho fry zooming around
    1. Rain event blows out your rig!

If you spied two wader-clad individuals climbing up and down the San Geronimo Creek banks this past week, it was our biologists rescuing their fishing trap!

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Interesting! I've hiked near there many times. It's great to see behind the scenes of the sampling process.

10 April 2017

Rainfall Measurements

  • April 6: 2.65 inches
  • April 7: 2.11 inches
  • April 8: 0.25 inches



6 April 2017
0800: Research assistant + coffee at the field site. Everything normal.


" What?"

A fkye net is a type of fishing gear. It is a net in the shape of a bag. The bottom of the bag (net) is anchored to the bottom of a stream bed and the top of the net is suspend open.

Fyke nets are commonly used by biologists to capture coastal and euryhaline species all over the world. The system is great because it causes minimal impact on by-catch (non-target species) and is not destructive to surrounding environment.

SPAWN uses ropes and t-posts anchored to the bank to hold open our fyke net.

As the picture shows: the mouth of the net is flanked on one side by wing walls connected to the creek bank. On the other side of the net, a low rock wall extends out about two feet, stopping short of the opposite bank. Allowing stream flow around the net is an important part of the mark recapture method fisheries biologists use to assess a population. Individuals in a population have to be "voluntarily" caught. Allowing stream flow around the rig enables any determined species to swim around our fish trap. This fishing trap design does direct most of the stream flow into the mouth of the net. The water current, and all accompanying creatures, travel to the back of the net and where the rig ends with a live trap box. The live trap box is made of PVC pipe and mesh.

Every morning SPAWN biologists, with the help of some rock star Citizen Scientists, check the live trap box.

The video shows a downstream view of SPAWN's fyke net before we attached the live trap---you can see how strong the creek was flowing!


How do you recruit your citizen scientists??

5 April 2017

11:00 SPAWN Biologists braved cold water to set up the fkye net.

18:30 Fyke net is set up!

Pictured is view from a bridge looking downstream.


A bit about the history of SPAWN:

Salmon Protection and Watershed Network (SPAWN) is a grassroots non-profit that has been monitoring salmonid summer habitat since 1999. SPAWN began monitoring the salmonid spawning activity on the six tributaries of San Geronimo Creek in 2001 and in 2006 added springtime monitoring of out-migrating smolts. SPAWN’s efforts are meant to support and complement the work of partners in the Lagunitas Creek Watershed including the CA Department of Fish and Wildlife, National Marine Fisheries Service, National Park Service, and the Marin Municipal Water District (MMWD).

You can find out more information about the organization at and find out about Volunteering Opportunities through Our Facebook Page or Smolt Monitoring Page

Expedition Background

The willingness for scientists to collaborate at local, county and state levels is crucial to developing strong, uniform protection for migratory species like salmonids.

In regards to Coho Salmon (Oncorhychus kisutch), Lagunitas Creek Watershed supports one of the largest remaining wild populations. SPAWN’s objective is to measure juvenile abundance spatially and temporally throughout in San Geronimo Creek and establish a baseline for how habitat restoration efforts are protecting and improving the population.

Coho are part of NOAA's Species in Spotlight Initiative

NOAA's Salmon Recovery Plan recognizes the importance of the Lagunitas Creek Watershed to the recovery of the entire population.


This is awesome Neely! I'm really excited to follow along and learn how you are structuring your assessment protocols. Thanks for sharing.