Salmon River Habitat Modeling
By: Justin Anderson, Britanie Castleton,
& Craig Larsen
Team
Responsibilities:
Justin
Anderson – History of Anadromous Fish Runs and Current Problems with Dams, Endangered
Species Act Issues and Regulations, Fisheries Research and Life Cycles,
Researched Historical Mean Monthly Flows, Helped with Catchment Calculations
and Analysis
Britanie
Castleton - Terrain Processing to Calculate Catchment Areas with GIS (Arc Hydro
Tools-spent many hours attempting but had problems with DEM, resorted to
ArcView data provided by the INSE), Data Collection from INSE and Filtering,
Habitat Sensitivity Analysis with GIS, and Computed the Flow to Catchment Ratio
Craig Larsen
– PHABSIM Output Interpretation (percent optimum), Hydraulic Cross Section
Analysis, Velocity vs. Cross Section Graphs, Flow vs. Percent Optimum Graphs,
& Recommended Flows, Research Historical Mean Monthly Flows
Introduction
The main focus of our project was to provide sustainable flows within the Salmon River. These sustainable flows were obtained by relating the channel hydraulics to the present fish species suitability curves. This relationship is displayed in a weighted useable area table and provides us with the percent optimal habitat for different increments of flow. We then did a study on the habitat sensitivity due to the change in flow for each month of the year. Finally, we devised a simple method that would allow us to make reasonable recommendation of flow on each reach within the Sawtooth National Recreation Area (SNRA).
To better understand the study undertaken a substantial amount of background information is given to help the reader understand why anadromous fish in the Stanley Basin are in jeopardy. This report lists why anadromous fish species are in decline, particularly in the Stanley Idaho basin. Using GIS and other computer program models we are able to model fish habitat by defining catchment areas, determining optimal flows for anadromous fish, looking at suitability in the river, manipulating data sets to determine flow hydrology and hydraulics, and habitat sensitivity. Three specific sites on the Salmon River were used to determine our analysis. This was done to specifically look at optimal flows and habitat that would sustain the native anadromous fish species, (Chinook Salmon and Steelhead) throughout their entire life cycles in the Stanley area. The Salmon River, near Stanley is particularly important for anadromous fish because of pristine spawning grounds and anadromous fish maturity.
Why Model Habitat?
On October 11, 1996, Congress passed the Sustainable Fisheries Act (Public Law 104-297) which amended the habitat provisions of the Magnuson Act. The re-named Magnuson-Stevens Act calls for direct action to stop or reverse the continued loss of fish habitats. Toward this end, Congress mandated the identification of habitats essential to managed species and measures to conserve and enhance this habitat. The Act requires cooperation among the National Marine Fisheries Service (NMFS), the Fishery Management Councils, and Federal agencies to protect, conserve, and enhance "essential fish habitat". Congress defined essential fish habitat for federally managed fish species as "those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity."
Not only does the Magnuson-Stevens Act call for the protection of fish habitat, but the Endangered Species Act (ESA) also calls for fish habitat protection.
Endangered Species Act
The Endangered Species Act (ESA) was enacted in 1973. Its purpose is to identify and conserve species of fish, wildlife and plants that are in a declining population to the point where they are now, or in the foreseeable future at the risk of extinction.
Under the ESA, species likely to become extinct in the foreseeable future are categorized as endangered; one likely to become endangered is categorized as threatened.
Hurting a threatened salmon or its habitat will become a federal crime punishable by a fine of up to $25,000 or a prison term of up to six months.
Why Model Habitat on the
Salmon River near Stanley Idaho?
Stanley Idaho, born steelhead and salmon make one of the longest spawning runs of any anadromous fish in the world. Juvenile fish ride the spring floods from Idaho's Sawtooth mountain streams to the Pacific Ocean, 900 miles to the west. After feeding on the ocean's riches for one to four years, adult fish fight their way back up the Columbia and Snake rivers, crossing eight huge dams, to return to pristine spawning streams. These long migrations created some of the strongest strains of ocean-run fish in the world.
Salmon River near Stanley,
Where is it?
The Salmon River
starts in Idaho’s Sawtooth Mountains.
Many tributaries quickly connect with the Salmon River to sustain yearly
flows. The Salmon River twists and
turns its way throughout central and northern Idaho until it flows into the
Snake River. The Snake River continues
a northwestward journey until it combines with the Columbia River. The Columbia River then empties into the
Pacific Ocean.
Digital
Elevation Model (DEM) of selected sites on Salmon River, SW 059, SW 127, &
SW 128
GIS Map of
Idaho Counties & Sawtooth National Recreation Area outlined
Anadromous fish in Stanley
Basin
Anadromous is greek (anadromous) meaning to run upward, from anadramein to run upward, ascending rivers from the sea for breeding.
Chinook Salmon Steelhead
The Chinook salmon is blue-green on the back and top of the head with silvery sides and white bellies; black spots on the upper half of its body with gray/black mouth coloration. Chinook salmon are generally up to 36 inches in length and weigh up to 30 pounds. Chinook salmon may spend between 1 to 8 years in the ocean before returning to their natal streams to spawn, though the average is 3 to 4 years. Chinook salmon spawn from late summer to late fall. Fry and smolts usually stay in freshwater from 1 to 18 months before traveling downstream to estuaries, where they remain up to 189 days.
When spawning, steelhead are a bright reddish color similar to a spawning rainbow trout. They tend to be more greenish in freshwater with small black spots on their back and most fins. Steelhead can grow up to 45 inches in length and 40 pounds in weight; although usually weighs less than 10 pounds and smaller than 32 inches in length.
Unlike salmon which die after spawning, steelhead may spawn several times. Because young steelhead spend a significant portion of their lives in rivers and streams, they are particularly susceptible to human induced changes to water quality and habitat threats. Migrating steelhead face the physical obstacles of high water temperatures resulting from dams, inadequate water flows in rivers and streams due to water diversions for irrigation, and the impoundment of water for power generation.
WHY DAMS KILL SALMON
Dams kill salmon because salmon must
migrate up and down the river to survive. Salmon are born in the gravel at the
bottom of fresh water streams. They grow to a few inches in the streams, then
must migrate downstream to the estuaries and out to the sea. They live in the
ocean for three to five years, before returning to their home stream to
spawn. Some dams were built with no way
for salmon to get either down or upstream.
Additional spawning habitat was
lost when rivers and streams were made into lakes. In total over 30% of the
habitat originally available to salmon has been lost. Adult salmon mortality may be due in part to trouble finding and
negotiating the fish ladders. The high
death toll for young salmon is caused, in part, by passage through the dam's
turbines. Some are killed directly by the turbines; others are stunned and
become easy prey.
Young salmon also die because of the dams causing changes in migration times. Salmon are genetically programmed for a one to two week swim to the sea, swept and shielded by the cold, cloudy, fast-flowing water associated with spring snow melt. Now, young salmon may take one to two months trying to find their way downstream. Longer migration in clearer, warmer water causes higher loss of salmon to predators. Salmon may even lose the urge to migrate.
Because Dams have catastrophically caused Chinook Salmon and Steelhead in the Stanley Basin to decline, it is even more important to keep spawning areas and juvenile habitat at optimal conditions. By modeling habitat we can ensure that native anadromous fish will be able to have the opportunity of trying to make it past the dams that cause them so many problems.
List of Dams causing problems for Stanley
Basin Salmon and Steelhead
Snake River Dams Columbia River Dams
Ice Harbor Bonneville
Lower
Monumental
Little
Goose
Lower Granite Mc Nary
Lower Monumental Dam
Chinook & Steelhead Lifecycles
Fry – Fish that have emerged from eggs
Juvenile – Young anadromous fish that makes the journey from fresh water to salt water
Adult – Mature fish coming from the ocean to spawn
Spawning Season – Where eggs are laid and fertilized in natal river and streams
Optimal Flows & Weighted Usable Areas
Throughout the year different species are present in the river and within each species different lifestages of fish are present. The factors affecting whether a fish is present or not during a particular time of year are stream velocity, depth, substrate, and temperature. For our analysis, velocity depth and substrate were the primary factors taken into account. To determine an optimal flow for each month of the year it must first be known which fish are present. The following charts display which fish are present at each of the three selected sites.
Site SW 059 0 = No Fish present 1= Fish Present
|
SW 059 |
|
J |
F |
M |
A |
M |
J |
J |
A |
S |
O |
N |
D |
|
CHINOOK SALMON |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Adult |
|
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
|
Fry |
|
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
|
Juvenile |
|
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
|
Spawn/Inc |
|
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
|
STEELHEAD |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Adult |
|
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
|
Fry |
|
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
|
Juvenile |
|
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
|
Spawn/Inc |
|
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
Source: INSE Lab
Site SW 127 0 = No Fish present 1= Fish Present
|
SW 127 |
|
J |
F |
M |
A |
M |
J |
J |
A |
S |
O |
N |
D |
|
CHINOOK SALMON |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Adult |
|
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
|
Fry |
|
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
|
Juvenile |
|
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
|
Spawn/Inc |
|
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
|
STEELHEAD |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Adult |
|
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
|
Fry |
|
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
|
Juvenile |
|
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
|
Spawn/Inc |
|
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
Source: INSE Lab
Site SW 128 0 = No Fish present 1= Fish Present
|
SW 128 |
|
J |
F |
M |
A |
M |
J |
J |
A |
S |
O |
N |
D |
|
CHINOOK SALMON |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Adult |
|
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
|
Fry |
|
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
|
Juvenile |
|
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
|
Spawn/Inc |
|
1 |
1 |
1 |
1 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
|
STEELHEAD |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Adult |
|
0 |
0 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0 |
|
Fry |
|
0 |
0 |
0 |
0 |
0 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
|
Juvenile |
|
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
|
Spawn/Inc |
|
0 |
0 |
1 |
1 |
1 |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
Source: INSE Lab
Each type of species and lifestage within a species will have different stream velocities, depths, and substrates that are preferred. As shown on the charts above there is always more than one lifestage within a species or species in the Salmon River at any given time of the year. Flows need to be determined that will be able to accommodate each fish type present and their preferred stream velocities, depths, and substrate conditions. Suitability Indices are used to show fish type preferences according to velocity, depth and substrate. A suitability index is a rating from zero to one, one being most suitable or preferred, at different velocities, depths, and substrates. The following are suitability curves for an Adult Steelhead Fish.
Suitability Curves for Adult Steelhead Fish
|
Substrate |
Code |
Size (inches) |
|
Organics/Grass |
1 |
- |
|
Silt |
2 |
<0.002 |
|
Sand |
3 |
.002-0.25 |
|
Fine Gravel |
4 |
0.25-1 |
|
Coarse Gravel |
5 |
1.0-3.0 |
|
Cobble/Rubble |
6 |
3.0-12.0 |
|
Boulder |
7 |
>12.0 |
|
Bedrock |
8 |
- |
|
Aquatic Vegetation |
9 |
- |
Source (Suitability
Curves): INSE Lab & State of
Each fish type has its own suitability curves. The other curves will not be shown in this report but can be accessed through this link: Suitability Curves.
River Cross Sections
With each fish type preferring a different flow, an overall flow that will result in the greatest benefit to the community as a whole must be determined. No flow that is determined for the community will be the most preferred flow for a given fish type. A type of bargaining must take place where fish types sacrifice a small amount of preferred conditions in order for the whole community to benefit.
Throughout the cross sections of the river different depths occur and the stream velocity changes over the course of the cross section. A cross section is separated into cells and each cell along the width of the river is deemed usable or unusable by certain fish types according to their suitability indices. Shown below is a cross-section split into cells and a velocity distribution located at site SW 128 (Click here for other cross-section and velocity charts). Notice that as the depth decreases the velocity will follow.
Source: INSE Lab
With the data previously discussed, namely fish presence, suitability indices, and channel cross-sections a weighted usable area (WUA) or percent optimum can be determined using PHABSIM.
PHABSIM is a computer program used to determine WUA’s according to the input data shown above related to the flow in the river. It relates the suitability indices of all the fish types, fish presence during a particular time of year, and flow rates. With this input data PHABSIM determines which of the cells along the river are usable by which fish type. This in turn is used to determine the WUA or percent optimum for the fish community as a whole, also done by PHABSIM.
The WUA or percent optimum is a percentage, 100% being the best, of how suitable the river is for the whole fish community while maintaining a certain flow. A percent optimum of 80% is desired as 100% will never be reached. The Fish must sacrifice a small portion of their preferred conditions according to flow so the whole community can have the majority of their preferences available. PHABSIM reports were obtained and with this percent optimums are known and the correlating flows.
Percent Optimum
versus Flow on a Monthly Basis At Site SW 059
Ideal Flow
Using the “Percent
Optimum vs. Flow” graphs, desired flows have been determined. These flows also take into account the mean
monthly flows. This is done in order to
determine a flow that will actually occur and not a flow that isn’t likely to
happen. The chart below shows the
“Ideal Flow” for each month of the year, the corresponding percent optimum, and
the actual mean monthly flows.
|
SW 059 |
JAN |
FEB |
MAR |
APR |
MAY |
JUN |
JUL |
AUG |
SEP |
OCT |
NOV |
DEC |
|
Mean Monthly Flows (cfs) |
6.41 |
6.04 |
5.92 |
15.58 |
69.07 |
93.98 |
43.2 |
10.6 |
5.67 |
6.37 |
7.65 |
7.46 |
|
Ideal Flow (cfs)
|
>17 |
>17 |
>21 |
>25 |
>48 |
>44 |
>36 |
>20 |
>20 |
>17 |
>17 |
>17 |
|
% Optimum |
60% |
60% |
60% |
60% |
80% |
80% |
80% |
60% |
60% |
65% |
60% |
60% |
At the SW059 site shown above, throughout much of the year the percent optimum is only at 60%. This is due to the actual mean monthly flows. 17-25 cfs are the corresponding flows to 60% Optimum, these flows are already much greater than the mean monthly flows. As can be seen, the actual flows need to increase dramatically throughout most of the year to even reach a mark of 60% optimum. It is possible, however, that the lower flows can be tolerated at this site. SW 059 is a stream called Yellowbelly Creek running into the Salmon River, it is not part of the main river reach; for this reason the conditions can be deemed tolerable.
Percent Optimum versus Flow on a Monthly Basis At Site SW 127
Ideal Flow
Site SW 127 is
located directly on the Salmon River and the flows are much greater than those
of SW 059. Maintaining higher flows
through the duration of the year gives us the opportunity to also maintain a
Percent Optimum of 80% year round. The
Ideal Flows are listed below.
|
SW 127 |
JAN |
FEB |
MAR |
APR |
MAY |
JUN |
JUL |
AUG |
SEP |
OCT |
NOV |
DEC |
|
Mean Monthly Flows (cfs) |
410 |
403 |
422 |
920 |
2,564 |
3,185 |
1,390 |
595 |
488 |
507 |
495 |
443 |
|
Ideal Flow (cfs)
|
285-755 |
285-755 |
336-1172 |
>389 |
>493 |
>545 |
>336 |
>336 |
>389 |
232-702 |
285-755 |
285-755 |
|
% Optimum |
80% |
80% |
80% |
80% |
80% |
80% |
80% |
80% |
80% |
80% |
80% |
80% |
Percent Optimum versus Flow on a Monthly Basis At Site SW 128
Ideal Flow
Site SW 128 is located on the main river reach and also yields a much larger flow than site SW 059. During the months of March and September, however, the 80% optimum mark was not able to be met. This was, as was the case at SW 059, due to the actual mean monthly flows in the river. 70% and 75% optimums, although 80% is preferred, are tolerable.
|
SW 128 |
JAN |
FEB |
MAR |
APR |
MAY |
JUN |
JUL |
AUG |
SEP |
OCT |
NOV |
DEC |
|
Mean Monthly Flows (cfs) |
214 |
230 |
222 |
343 |
1,093 |
1,765 |
819 |
347 |
255 |
248 |
252 |
244 |
|
Ideal Flow (cfs)
|
200-1570 |
221-1571 |
>220 |
292-2210 |
>363 |
292-1996 |
292-1570 |
292-1570 |
225-2200 |
150-1144 |
221-1570 |
221-1570 |
|
% Optimum |
80% |
80% |
70% |
80% |
80% |
80% |
80% |
80% |
75% |
80% |
80% |
80% |
Habitat Sensitivity to Flow
Analysis
From the WUA tables we can relate the mean monthly flows to the percent optimum habitat with GIS tool. The sensitivity was measured by decreasing the mean monthly flow by 10% increments from 100% to 50% to represent the affects of a possible diversion. Generally, you want your percent optimal habitat to be 50% or higher, however, this percentage will vary based on the characteristics of the river.
Digital
Elevation Model (DEM) of selected sites on Salmon River, SW 059, SW 127, &
SW 128
On the Salmon River Site 3 or SW 128, which is a big river sites averaging around 700 cfs, we can see on the charts below in a comparison of May, a high flow month, to September, a low flow month, that the percent optimal habitat, the green chart, stays relatively high even with the incremental decreases.
Salmon River Site 3, SW128
The Salmon River Site 2 or SW 127-averages around 500 cfs and has a similar reaction to SW 128.
Yellowbelly Creek or SW 059- 30 cfs, greater fluctuation can be observed in flow and percent optimum.
To see each site for its year round sensitivity please see power point presentation.
As you can see from this analysis smaller site are a lot more sensitive to changes in flow than larger sites. This is due to the construction of the WUA tables with the SI curves and the respective changes in velocity and depth of the water. Larger river are generally wider and have a more flat channel bed, thus, the changes in the velocity and depth will not be as dramatic as they would in a smaller channel where the bed has a greater effect on the hydraulics.
Recommended Flows
Our objective is to provide recommended instream flows for any reach within the Sawtooth National Recreation Area. By recommended I mean the minimum allowable flow to maintain habitats adequate for the species and life stages of fish present for that time of year. To do this we have our recommended flows based on the WUA tables for our three study sites shown above. Then, by using the Arc Hydro Terrain Processing tool like we did in exercise 5 you can calculate the drainage area from the DEM for each site. After many hours of working on the reconditioning and other steps of the processing of the DEM we encountered many errors and couldn’t find any helpful resource as to the reasons why. Therefore, we resorted to using catchments produced from the INSE. From there we simply calculated a flow to drainage ratio, which can then be applied to any other site within the area.
To calculate the drainage areas we used an extension in ArcView called XTools. The area for the Salmon River Site 2 is 215,548 acres and the recommended minimum flow is 389 cfs. So the flow to catchment ratio is 389 / 215,548 = 1.8 E -3
To calculated the minimum recommended flow for 4th of July Creek, a tributary to the Salmon River, the drainage area is calculated at 12155.9 acres and multiplying this by the flow to catchment ratio 1.8 E-3. Which gives a flow of 21.9 cfs.
Problems Encountered
This is a pretty basic analysis, otherwise known as “quick and dirty”, however, as simple as it may seem this assumption is not that far-fetched and will provide a reasonably accurate flow. Of course, this leads to another assumption that says that the same species and life stages of fish are percent in every reach of the entire system year round. This may or may not always be the case, just because there are Steelhead present in one stream does not automatically mean that they are present in another stream. However, with our analysis base on the community of fish we get a good average of what is really going on in the system.
Another area of concern was the study site locations. Looking back from the now finished project we wish we would have pick site that were more representative of the area as a whole. Two of our sites were on the main steam Salmon River and the other just upstream of a connecting tributary and just down stream of a lake. Ideally, we would have picked a few different sites with varying drainage areas, and channel characteristics that represent the majority of the streams within the area. However, if we are only considering the Salmon River and immediately connected tributaries this analysis is very sensible.
Water Resource Applications
and Conclusion
This kind of analysis is very useful for water right adjudications, protection of endangered and threatened species, locating optimal diversion points and/or channel maintenance analysis.
The INSE in 1998 did a similar study on a much larger and more detailed scale on the SNRA. The main purpose was to provide the State of Idaho’s Division of Water Resources with sustainable flow to protect the endangered anadromous fish within the area. They also recommended optimal points of diversion in area where there where high water right demands and provide a channel maintenance study.
Through our analysis we were able to apply the hydraulic and habitat models completed by the INSE and do our own smaller scale analysis.
References
INSE Laboratory, “SNRA Project” INSE Laboratory-Utah State University (1998)
Essential Fish Habitat, November 11 2002. An Introduction to Essential Fish Habitat
http://www.psmfc.org/efh/efh.html
National Marine Fisheries Service, November 11 2002. Chinook Listing Status Map
http://www.nwr.noaa.gov/1salmon/salmesa/chinesum.htm
National Marine Fisheries Service, November 11 2002. Snake River Spring/Summer Chinook Salmon ESU
http://www.nwr.noaa.gov/1salmon/salmesa/maps/chinsrss.pdf
Idaho Steelhead and Salmon, November 12 2002. Idaho Steelhead and Salmon
http://www.idfishnhunt.com/steelsal.html
Idaho Department
of Water Resources, November 15 2002. Statewide
Data List
http://www.idwr.state.id.us/gisdata/data_lists/datalist_statewide.htm
Jacqueline Harvey, November 15 2002, Sawtooth Fish Hatchery
http://imnh.isu.edu/digitalatlas/geog/fishery/hatchery/sawtooth.htm
U.S. Department of the Interior, U.S. Geological Survey, Nov.-Dec.2002. Real-Time Water Data
http://water.usgs.gov/realtime.html
Should we breach the Snake River Dams, November 15 2002.
http://www.theslowlane.com/91tripb/gen.html
National Marine Fisheries Service, November 11 2002. ESA Listing Maps
http://www.nwr.noaa.gov/1salmon/salmesa/mapswitc.htm