2019 Estuary Survey

Sungnome in a canoe documenting bathymetric survey data

This year’s topographic survey was completed using Photogrammetry and a sUAS (aka Drone). We achieved an excellent absolute accuracy using this process along with about a dozen RTK surveyed Ground Control Points (thank you Conor Shae of the USFWS). In addition to a much more accurate survey, we also reduced costs as compared with a more traditional total station survey like we did in the past. The Estuary is ideal for drone mapping missions as the terrain is fairly flat and open. A total of nine flights at 300 feet altitude AGL (Above Ground Level). 

We conduct surveys as often as possible to collect the following data:

  • Topography of the estuary
  • LWD survey to identify large wood placed with a helicopter in 2013 & 2016
    • All placed wood had pit tags installed so we are now able to scan those tags to identify pieces of wood and track their movement
  • Bathymetric survey to identify pools and collect pool data

Download the Draft Final Report

A draft report was completed and is available for download here.


Josh Madrone standing on back side of Woodzilla2 in June 2019. Several feet of gravel has been deposited here, burying multiple logs and 5 ton boulders.

Overview and Intent of Proposed Action

Restoration of fish habitat in the Mattole River estuary requires a comprehensive multi-year approach. The approach presented here is driven by a set of biological objectives, which, in turn, are controlled by various physical processes at work in the lower Mattole River.

The biological objectives of this effort are to:

  • Improve juvenile salmonid survival during summer, low-flow periods
  • Increase availability of suitable winter rearing habitat, with emphasis on juvenile coho salmon winter refuge habitat.

To accomplish these objectives, this five-year strategy seeks to integrate our understanding of the dynamic nature of the lower river by identifying a suite of physical river features for treatment.

The intent of these treatments has several physical objectives:

  • Increase channel stability in the lower Mattole River
  • Increase instream habitat complexity
  • Promote riparian vegetation colonization and growth
  • Create a mosaic of varying streambed sediment sizes
  • Promote more variable topographic diversity in the reach
  • Increase connectivity to existing sloughs, alcoves, and other off-channel habitat
  • Increase stream nutrients available to native species

Finally, recognizing the dynamic setting of the lower Mattole River and our ever-improving understanding of riverine processes, the proposed action is intended to be adaptive. The adaptive elements of the plan are described in detail at the end of the proposed action section.

Three specific types of projects are proposed here:  placing structures on islands; installing structures at the apex of river bars; treatments along the margins of river terraces; and re-connecting a slough channel to the estuary. The specific treatment locations and types are described in detail below.

Monitoring Background

This follows monitoring work done in 2014, summer 2017, and now again in summer 2019. The 2019 survey was completed by Josh Madrone and Sungnome Madrone. A drone was used for topographic and bathymetric information combined with ground surveys of pool length, width, and depths, and locations of large wood/whole trees.

Previous Surveys

The two previous surveys were done by Total Station ground surveys, to survey features such as large wood/whole trees, stream barbs, structures, pools, and major topographic breaks. The 2014 survey was completed by Keith Barnard, Sungnome Madrone, and ________________. The 2017 survey was completed by Keith Barnard, Sungnome Madrone, Josh Madrone, and Brandon Madrone.

Survey Dates

The 2014 survey was completed in October, between the 7th and 30th. The flow at time of getting pool data was ~20 CFS. In 2017 we surveyed once around the 19th of May and again on the 1st of June. The flow at that time was between 240-380 CFS. In 2019 we surveyed on June 7th and again on September 13th. Pool data was collected with a flow of ~35 CFS.

Table 1. Survey dates and river flow


Survey dates

River flow (CFS)



October 7



October 30




March 13-14



May 17-19


Pools 1-16

June 1-2


Pools 17-19


June 7



September 13


Pools 1-14 (all)


Report Focus

This report will focus on the monitoring results from the summer 2019 survey for tree locations after 3-6 years of flows and rearrangement of large wood, as well as the location of pools in this lower river reach/estuary.

UAV Mapping (Photogrammetry)

Photogrammetry is the science of obtaining reliable measurements from photographs and digital imagery. The 2019 aerial imagery was collected with an Unmanned Aerial Vehicle (UAV) – DJI Phantom 4 Pro v2 – with a 20 Megapixel camera, flying ~300 ft Above Ground Level (AGL). The resulting photos were processed in Agisoft MetashapePro v1.6.0 to create 3D spatial data to be used in GIS applications. The two primary outputs that were created and exported are a georeferenced orthomosaic, commonly used in geographic information systems (GIS) as a “map accurate” background image, and Digital Surface Model (DSM), which gives you the height of the objects that are on the surface of the earth. These files are saved in the most-GIS-compatible GeoTIFF format. Ground Control Points (GCP) were surveyed with RTK GPS by Connor Shae of USFWS, which were used in the reconstruction of the model, with a few saved for check points to measure the accuracy of the finished model.

3D Model in Agisoft MetaShape Pro

This year’s topographic survey was completed using Photogrammetry and a sUAS (aka Drone). We achieved an excellent absolute accuracy using this process along with about a dozen RTK surveyed Ground Control Points (thank you Conor Shae of the USFWS). In addition to a much more accurate survey, we also reduced costs as compared with a more traditional total station survey like we did in the past. The Estuary is ideal for drone mapping missions as the terrain is fairly flat and open. A total of nine flights at 300 feet altitude AGL (Above Ground Level). 

A draft report was completed and is available for download here.

Treatments Implemented

In Fall 2013 and again Fall of 2016 hundreds of whole trees were put into the estuary. Details are included in the Final Reports for those projects.

The 2016 helicopter wood placement component for this 2016 work included the following numbers of whole trees placed:

Table 2 – 2016 wood placement stats

Area L-1

12 pcs

Area L-2

9 pcs

Area R-1

9 pcs

Area R-2 and R-3

31 pcs

Area R-4

22 pcs

Area R-5

11 pcs

Woodzilla 2

9 pcs


103 pcs


A total of 103 pieces placed in-stream, at terrace margins, or on the right bank (nearly all were Whole-trees, with boles and integral root wads). Plus, approximately another 150 pieces were delivered to the south-side terrace — to sites L-3 and L-4, located upstream from the 2013 project area — and subsequently used for stream barbs (small to medium-sized trees, some without root wads). Trees were tipped on-slope with an excavator and placed in the river by helicopter. Total acres of riparian area treated was 20. Over 2000 15-foot long willow cuttings were planted in the deep trenched baffles.

We constructed 30 stream barbs with 160- 60 to 80-foot-long trees that were 16-36” in diameter with root wads and limbs. The total trench length was 2740 feet with 3,340 willow cuttings 15- 20 feet long and multi branched. The stream barbs treated 2010 feet of stream bank. This approach uses a bio-technical terrace margin treatment designed to increase bank resistance to erosion. The trenches were placed at about a 30-degree angle downstream with the flow and about 50-70 feet apart. The trenches were excavated 15-20 feet deep to the summer water table so that the cuttings were placed in water immediately after being cut. After backfilling the trenches, the area was regraded and mulched.


Monitoring Program

After tree placement was complete, the Mattole Salmon Group implemented a monitoring program to answer the question,” Which trees moved, under what size flows, and where.” This monitoring program involved placing a Passive Identification Tag (PIT) into each whole tree. A hole was drilled with a cordless drill at 4’ above root wad. The hole was drilled towards the center of the log, and at a depth to put the tag ½ inch under the cambium. The tag was inserted into the tree (see figure 5). Silicone calk was used to seal the hole and secure the tag. Trees with greater than 16” diameter got two tags, on opposite sides of the tree.  Additional information was collected about size (total length and diameter at breast height (DBH), species and complexity for each tree and associated with the trees individual number. Using a total station all trees were marked in their orientation on the landscape. 


The total station work gave us an as built map of the entire project site with one (1) foot contour intervals.

Two re-surveys have taken place since the project began.  One in the spring of 2014, and another in the Spring of 2017. Re-surveys involve scanning the tree PIT tags and using GPS to locate each tree on the project map. This shows which trees have moved and to where. We used a total station to re-map terrain elevations after many significant high flows (over 25,000 CFS) during 2016-2017.


Large Wood / Whole-Trees

The 2019 large wood survey found 64 pieces of large wood.

However, the actual number is greater because there are multiple structures with multiple pieces of large wood in them, which were recorded as a single piece (eg. Woodzilla 2 structure is 9 whole-trees).



In 2012 there were 8 pools 3-5 feet deep in the treatment reach. After the placement of the 2013 and 2016 heliwood trees, and after high flows of 2016/2017, there were 20 pools that were 5-12 feet deep in the same reach. All pools were in close association with the placed heliwood.

In 2019 there were 14 pools that were 4-10 feet deep (see Figure 7) It should be noted that a more restrictive definition for pools was implemented in 2019, which if used in previous surveys would have resulted in fewer pools. One goal in 2019 was to standardize definition of pools going forward to be able to easily replicate in the future.

Pool Definition

For our purposes, Pools are defined as a small part of the reach with reduced velocity, little surface turbulence and deeper water than surrounding areas. To be considered a pool for this survey, the maximum depth at the deepest point was a minimum of 4 feet. Additionally, pools have the following characteristics:

    1. a surface slope of 0%,
    2. a hydraulic control,
    3. a maximum pool depth >=4 ft, and
    4. often form around boulders or large woody debris,


Table 3 – 2019 Pool Measurements

Pool #




Volume (ft3)




































































Total volume of pools (ft3)



Pool locations are shown in Figure 7. Full size maps are available on the file server as geo-referenced PDFs ready to print at full-resolution up to Tabloid size (11×17).


The final map (see figure 8) shows large wood as placed as well as movement between surveys. This is a draft copy of this map and will be replaced in final version.


Flight Mission Planning

My workflow involves a multi-step process using a few different apps. Flight mission planning and image acquisition is done with Pix4D Capture using a DJI Phantom 4 Pro V2.

Post image processing and dense point cloud are created with Agisoft MetaShape Pro. Final maps are produced using QGIS on a Mac.

Sample Flight Mission Plan in Pix4D Capture

Photo Gallery

2015 Summer Steelhead Dive – July 17-18th!

The 2015 Mattole summer steelhead dive will be Friday July 17th and Saturday July 18th.  Conducted annually since 1996, this watershed-wide survey is our primary source of information on the abundance and distribution of adult summer-run steelhead, and also provides information on the distribution of other native and non-native aquatic species. For more information check out our Summer Steelhead Dive page.

We are excited to host this year’s dives again at the beautiful A.W.Way county park. We will have a camp site reserved with limited tent space available for Friday and Saturday night. We will be asking divers for a $5-10 donation to help us offset the costs of camping and day-use fees. There are flush toilets, hot showers and an awesome swimming hole!

For more information and to sign up, please contact Michelle Dow (michelle@mattolesalmon.org).

PLEASE RSVP by July 7th.

Return of the Kings!

Many Mattole watershed residents know that spending some time at the right spot on the river in the fall and early winter can yield sightings of Chinook (also called King) salmon as long as your leg. They’ll be swimming lazy circles in deep pools waiting for the next storm to move upriver; or on the spawning grounds, females working their tails literally to the bone to move grapefruit sized stones to ready the streambed for their eggs, while the males, all spots and scales and teeth and leering eyes and blind aggression are chasing each other about for the chance to fertilize those eggs.

Less well appreciated is that much of the Mattole River is also alive with Chinook in the spring. These fish, the progeny of the single-minded adults from the winter before, are much less conspicuous than their forebears, since they are only a few inches long. But they are much more numerous, with literally hundreds of thousands of them headed out to sea every spring.

MSG staff have been conducting regular dives in a river reach downstream from Petrolia beginning in April of this year, in part to monitor juvenile salmon and steelhead use of recent restoration projects. We’ve seen large numbers of juvenile Chinook, literally thousands, in just a short stretch of river (a few pools).

While this is just a snapshot of conditions in a small portion of the watershed, these observations seem to suggest that spawning incubation, and fry emergence from the relatively strong Chinook run from the winter of 2014-15 was fairly successful. We would expect this to be so, given that December rains allowed the bulk of the Chinook run to move upstream into tributaries and the mainstem in the upper portion of the watershed, reaches with generally more favorable spawning conditions than the lower river, and the subsequent mild flows and lack of large storms probably led to high rates of survival of eggs and fry.

Juvenile Chinook have a strong preference for areas with woody cover (such as willows or alders dragging in or fallen into the water) and relatively low velocity adjacent to higher velocity areas suitable for drift-feeding. Juveniles are concentrated in these spots, and generally absent elsewhere – although in the last couple weeks, we’ve seen more Chinook out away from cover feeding in riffles and more open water, presumably due to the combination of declining flows leading to more areas with suitable lower velocities, and larger fish with increasing ability to hold in faster water and less of a cover preference as they grow.

Another pleasant surprise on dives in late April and early May were observations of numerous coho smolts. Seeing a coho salmon smolt in the lower Mattole River feels a bit like finding the proverbial needle in a large and dimly lit haystack. Seeing a dozen in one pool is better!

For the sake of all these fish, hopefully temperatures remain mild, we get some more early summer rain, and all of us Mattole bipeds do our part to conserve water and keep more in the river.

Mattole Salmon Group 2014-2015 Spawner Survey Update

2014-2015 Mattole Salmon Group spawner surveys have been underway since early November (2014) and are about to conclude for the season. Here is a recent update of this year’s spawner survey observations. This data is preliminary so please view it as such.

As of February 10th, MSG surveyors had observed 80 Chinook redds (salmon nests), 4 coho redds, 72 steelhead redds, and 19 additional redds which were unidentifiable to a species. As of the same date, we have surveyed 15 reaches, which is around 20% of the total sample frame.