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).

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April 8 2017


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Mission Underway

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!

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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?"

Neely 1 comment

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!

Neely 1 comment

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!

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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.

Neely 1 comment

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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Neely 1 comment

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


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

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" 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!

Neely 1 comment

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.

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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

Neely 0 comments
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.

Neely 1 comment

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