South Fork Snake River Macroinvertebrate Study 2019

Updated: Jun 2, 2021


  • February 2019, we began our long-term monitoring of aquatic macroinvertebrates (insects and other creatures that live in the river bottom) in the South Fork Snake River by sampling sites representative of the Upper South Fork, South Fork Canyon, and Lower South Fork.

  • Abundance of macroinvertebrates averaged roughly 134,000 individuals per square meter across all sites.

  • Mayflies, stoneflies, and caddisflies composed roughly 10-35% of all individuals within South Fork samples.

  • Aquatic habitat quality in the Upper SF and Canyon SF was “good” to “fair”, while aquatic habitat quality in the Lower SF was “fairly poor”, based on a standard index.

  • Relative to the Henry’s Fork in 2019, the South Fork had more macroinvertebrates per square meter, lower diversity of macroinvertebrates, similar abundances of mayflies, stoneflies, and caddisflies, and poorer aquatic habitat quality.

  • This data provides great baseline information on aquatic macroinvertebrates and habitat quality in the South Fork Snake River and will be critical for monitoring and identifying changes in future conditions.

Dr. Rob Van Kirk wrote an excellent blog regarding the “Who”, “What”, “When”, “Where”, “Why”, and “How” of aquatic macroinvertebrates in the Henry’s Fork. Many, if not all, of the background details to the Henry’s Fork macroinvertebrate study could seamlessly describe and explain our approach to South Fork Snake River study. Rather than re-invent the wheel, you can find that information here. South Fork-specific information is below.

I included 2019 Henry’s Fork macroinvertebrate data in all the figures and much of the discussion. I did this to provide context for the South Fork data, not to try to discern “which river is better?” Comparing the South Fork and the Henry’s Fork is almost an apples-to-oranges comparison. Even though they are geographically close, have similar species, and are both fantastic fisheries, they are influenced by very different geological and morphological conditions (e.g. one is largely spring-fed, one is several magnitudes larger than the other, etc.), as well as by different water management operations. The goal of this long-term monitoring is to; 1) understand the current composition and abundance of macroinvertebrates in the South Fork, 2) relate macroinvertebrate communities to aquatic habitat quality, 3) monitor macroinvertebrates on an annual basis to identify if conditions are changing, and if so, what environmental conditions might be driving the changes.

Background Information

Why monitor macroinvertebrates?

Aquatic macroinvertebrates are the workhorses of aquatic ecosystems. They convert primary energy sources such as plants and algae into trout food, providing the majority of the diets of young trout. Although large trout—especially brown trout—can get a large fraction of their energy from vertebrate prey such as small rodents and fish, in the Henry’s Fork and South Fork, even adult trout continue to feed primarily on invertebrates. Of course, without aquatic invertebrates, fly fishing would be a completely different activity. Although many popular fly patterns imitate vertebrates and terrestrial insects, the majority of trout fly patterns imitate the various life stages of aquatic invertebrates, primarily mayflies, stoneflies, and caddisflies. As it turns out, these insects are indicators of water quality and overall health of the aquatic ecosystem because most species of mayflies, stoneflies and caddisflies are sensitive to water pollution and habitat degradation. In fact, this group is so important in the assessment of water and habitat quality that it has its own acronym among aquatic ecologists—EPT. This acronym is short for the three taxonomic orders Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies). Higher relative abundance of EPT taxa indicates better water and aquatic habitat quality. Several other quantitative measures calculated from the relative abundance of different taxa complement the EPT percentage to provide indexes of the quality of aquatic habitat. Although HFF maintains an extensive network of water-quality monitoring equipment throughout the watershed, water quality measurements give us data only on the physical and chemical composition of the water itself and not on the quality and quantity of aquatic habitat. Aquatic invertebrates integrate habitat quality and water quality to indicate the overall quality of aquatic ecosystems. Because of this, monitoring of aquatic macroinvertebrates has become the standard method for government agencies, scientists, and organizations like HFF to keep track of trends in aquatic ecosystem health.

What macroinvertebrate monitoring CANNOT tell us

Many aquatic macroinvertebrates, such as leeches, worms, and snails, spend their entire lives in the water. Others, such as most aquatic insects, have both an aquatic and a terrestrial life stage. In fact, the adult stage of common mayflies, stoneflies, and caddisflies provides the most sought-after angling opportunities on the Henry’s Fork and South Fork—the chance to catch a trout on a dry fly. However, the adult stage of all aquatic insects is very brief compared to the aquatic stage—a few hours to days on land compared with months to years on the stream bottom. As a result, effective sampling of aquatic macroinvertebrates and use of macroinvertebrate measures to tell us about habitat quality relies on sampling the invertebrates while they are in the river—not in the air. That is, aquatic insects are sampled as nymphs or larvae, not as adults. Therefore, the analysis of aquatic macroinvertebrates does NOT tell us anything about a particular hatch of adult insects from a fishing standpoint, especially on any particular day or location in the river. In general, the fishing-related aspects of adult insect hatches are only very loosely related to abundance of the aquatic (nymph) stages and depend on a lot of other factors such as weather, streamflow, fish behavior, and water clarity.

So, I can only describe our aquatic invertebrate sampling and what it tells us about overall aquatic habitat quality; knowing full well that what I report will contradict the personal fishing experience of many anglers. This is because, as explained above, the aquatic invertebrate analysis provides information on aquatic habitat quality, and does NOT reflect hatches of adult insects from a fishing standpoint. This certainly won’t be the first time that what I report from a scientific standpoint is inconsistent with angler experience on the river.


HFF staff and HFF volunteers collect the invertebrate samples, with the direction of Brett Marshall, an experienced invertebrate biologist who runs a company called River Contiuum Concepts in Bozeman. Brett has been known as “The Bug Guy” for over two decades and is a national authority on aquatic invertebrates. His consulting firm specializes in assessment of aquatic ecosystems. Brett and his team process the samples and provide the data to HFF. Brett also maintains a “master list” of all aquatic invertebrates HFF and its partners have ever found in the Henry’s Fork Watershed and now the South Fork Watershed, updating scientific names as necessary to keep pace with advances in identification and taxonomic classification. HFF staff then use statistical methods to analyze the data.


Most aquatic invertebrates have a well-defined life history driven by seasonal patterns in day length, water temperature, streamflow, and other environmental factors. Other than midges, which hatch and reproduce year-round, most aquatic insects in the Henry’s Fork and South Fork hatch and reproduce during the spring, summer and fall—roughly between the middle of March and early November. In addition, most of the common EPT taxa have a one-year life cycle, meaning that immediately after hatch of a particular insect, that species is represented on the stream bottom only by eggs or very young individuals, which are too small to be sampled and counted. For example, if we sampled in mid-July, we would be very unlikely to capture any green drakes in our sample, because this year’s cohort would have just hatched, and next year’s are still in the egg stage. For the South Fork, sampling occurred over two days (one day to sample the upper reach and lower reach; one day to sample the canyon reach) at the end of February in order to sample before flows potentially increase for flood control. We will continue to sample at this time each year in order to obtain the most complete sample of all species in a consistent manner.


Three South Fork sampling sites were selected to represent the ecologically and geologically unique reaches that comprise the South Fork. The first sample location was representative of the “Upper Reach” (roughly Palisades Dam to Conant boat ramp) and was conducted below the highway bridge near Spring Creek boat launch. Conditions at this location are primarily influenced by discharge from Palisades Dam and two major tributaries (Palisades Creek and Rainey Creek). This site is also located just prior to a geological and morphological transition from wide braided channels to one predominant main channel that continues through a 25 mile stretch of canyon. The next location represented the “Canyon Reach” (roughly Conant boat ramp to Byington boat ramp) and was sampled near Lufkin bottom camp. This section of river is dominated by a canyon landscape with a relatively restricted fluvial plain. The last sample location for the “Lower Reach” (roughly Byington boat ramp to the confluence of the Henry’s Fork) was conducted near Lorenzo boat ramp. This section has numerous side channels and a very active flood plain. After high water years, it is not uncommon to have significant alterations to the main channel and side channels, as well as various gravel bars and areas with large woody debris.


Macroinvertebrates are collected using what is called a Hess sampler, which is basically an open aluminum drum that is pushed down into the stream bottom. The substrate on the bottom of the stream is then vigorously stirred to free the invertebrates living there. The drum has a screened opening on one side that allows water to flow into the sampler, and a mesh net across from the opening captures the invertebrates as they are stirred up from the bottom and flow into the net. All large rocks that are present within the area sampled by the drum are manually cleaned with a brush to make sure all invertebrates (especially case-making caddisflies) are scraped into the sampler. The drum has a known area so that the number of invertebrates in the sample can be extrapolated to abundance per square meter of stream bottom. We collected six samples at each site to account for variability across the stream bottom and increase statistical power during data analysis.

Each sample is emptied out of the net and into a plastic jar and then preserved with alcohol. At Brett’s lab, the sample is cleaned and sorted, to separate the invertebrates from sand, gravel, and plant material. Individual invertebrates are then identified and counted. In samples from the Henry’s Fork and South Fork, which contain very large numbers individuals, only a subsample of each full sample is used for counting and identification. Brett aims for identification of about 200 individual invertebrates from each sample, and he uses a strict quality-control procedure. After a sample is processed, a second technician sorts the sample to validate the result of the first technician. If there are discrepancies, a third person examines the sample. As a result, Brett’s lab is known for providing the highest level of accuracy and precision in quantitative analysis of invertebrates; he consistently finds more small organisms in samples than is the standard in the industry.


Brett’s lab reports raw data, which consists of the number of each identified taxon present in each sample. He also reports summary data such as total number of individuals per sample, number of different taxa, number individuals in the sample from the EPT taxa, and various indicator metrics. We have focused on four different metrics:

  1. Abundance (number of individuals per square meter of stream bottom)

  2. Shannon’s diversity index (higher diversity means more individuals spread across a larger number of different taxa)

  3. Percent EPT (fraction of total number of individuals that are mayflies, stoneflies, and caddisflies), and

  4. Hilsenhoff Biotic Index (a measure of habitat and water quality)

What Did We Learn About the South Fork?


Abundance of macroinvertebrates was very high in the South Fork Snake River, averaging 134,000 individuals per square meter across all three sites. Average abundance of macroinvertebrates was lowest at the Upper SF site (94,000 individuals/m2) and increased further downstream, with the highest abundance at the Lower SF site (average 173,000 individuals/m2). Variability was high between replicates samples within sites, evident by the wide confident intervals in the figure below, making it difficult to determine if there were statistically significant differences between South Fork sites. The high variability between samples is likely a product of diverse substrate and ecological conditions within each site, and additional replicate samples will be taken in 2020 to try to increase the statistical power of the data.

Compared to macroinvertebrate abundances in the Henry’s Fork in 2019, average abundance of macroinvertebrates on the South Fork was four times that of the Henry’s Fork. That being said, the total abundance of macroinvertebrates doesn’t tell the full story of macroinvertebrates between the two rivers, as the proportions of the macroinvertebrates were very different. More on this below in the “Percent and abundance EPT” section.


Shannon’s diversity index is a common metric used in ecology to describe the diversity of organisms within a system. Essentially, the maximum Shannon diversity index is achieved when there are equal abundances of individuals for each taxa present. This maximum number increases as more taxa are present. For example, a sample with 50 individuals of Taxa A and 50 individuals of Taxa B would have a higher Shannon’s diversity index than a sample that had 90 individuals of Taxa A and 10 individuals of Taxa B. Additionally, a sample that had 25 individuals of Taxa A, 25 individuals of Taxa B, 25 individuals of Taxa C, and 25 individuals of Taxa D, would have a higher Shannon’s diversity index than a sample with 50 individuals of Taxa A and 50 individuals of Taxa B. See this link for a full description of the Shannon diversity index.

Diversity on the South Fork was lowest at the Upper SF site (diversity index 2.48) and increased with distance downstream. The Upper SF site is influenced by the relatively cool, consistent, and presumably low-nutrient water coming out of Palisades Dam. Additionally, the substrate is likely more homogenous in the Upper SF due to scouring of smaller materials (gravels and cobbles) below Palisades Dam without the opportunity for transport of new substrate material from upstream. As you progress further downstream from Palisades Dam, it is likely that water temperatures increase, more nutrients become available and substrate composition becomes more diverse due to additional tributary contributions and bank erosion, more woody debris is present in the river, and there is higher diversity of habitat. Similar trends have been documented on the Henry’s Fork. Spring-fed, headwater habitat near Flatrock has the lowest macroinvertebrate diversity in the Henry’s Fork and macroinvertebrate diversity increases with distance downstream.

Percent EPT and abundance EPT

Percent EPT is the percent of the individuals at the site that are mayflies (Ephemeroptera), stoneflies (Plecoptera), and caddisflies (Trichoptera). The Upper SF site had the highest percent EPT (average 35%) and the Lower SF site had the lowest percent EPT (average 10%) in the South Fork.

Relative to the Henry’s Fork, the South Fork has much lower percent EPT. The Upper SF site, which had the highest percent EPT on the South Fork, was comparable to the Ora site on the Henry’s Fork, which had the lowest percent EPT (average 31%) on the Henry’s Fork. Generally, percent EPT is a reflection of habitat quality and substrate composition. A decrease in percent EPT, and subsequently an increase in non-EPT species such as midges and worms, typically correlates with increased amounts of fine sediments and poorer habitat quality. Even though the percent EPT is much lower on the South Fork relative to the Henry’s Fork, the total abundance of EPT species in the South Fork is comparable to the total abundances of EPT species in the Henry’s Fork.

Biotic Index

The Hilsenhoff biotic index (HBI) is a metric that classifies habitat quality using the tolerance levels to organic pollution and habitat degradation for macroinvertebrate taxa found at the site. This is done by scoring taxa from 0 (intolerant to degradation) to 10 (tolerant to degradation), then averaging the scores of macroinvertebrates in the sample. Higher HBI scores (higher abundances of species with greater tolerance to habitat degradation) indicates lower aquatic habitat conditions. Conversely, lower HBI scores (higher abundances of species with lower tolerance to habitat degradation) indicates better aquatic habitat conditions. Click here for a complete description of HBI.

The Upper SF and Canyon SF had “good” to “fair” habitat classifications while the Lower SF was classified as “fairly poor” habitat. This HBI classification shouldn’t come as a surprise knowing that the abundances of EPT taxa (species with low tolerance to degradation) decreases with distance downstream while overall abundance of macroinvertebrates increases with distance downstream. Additionally, it shouldn’t come as a surprise that the Henry’s Fork has lower HBI scores compared to the South Fork. The Henry’s Fork is a smaller order river that is greatly influenced by cold, clear, clean, and relatively consistent spring water. Additionally, the dams on the Henry’s Fork are also much smaller and likely don’t impact downstream habitat as much as Palisades Dam.

Concluding thoughts

The South Fork has high densities of macroinvertebrates throughout the river. Abundances and proportions of macroinvertebrates change from the Upper SF to the Lower SF. Most notably, abundances of midges, worms, and other species that have higher tolerance to organic pollutants and habitat degradation increase with distance downstream. For folks that have floated the entire river, this probably doesn’t come as a surprise. As you travel downstream from Palisades Dam, the amount of fine sediment filling interstitial space in the substrate and amount of periphyton covering the substrate increases.

For folks familiar with the River Continuum Concept, the macroinvertebrate communities in the South Fork are what you might expect. In most free-flowing river systems, as you travel further from the headwaters the amount of nutrients in the system increases, the amount of sunlight making it through the canopy to the substrate increases, river velocity decreases, water temperatures increase, and overall primary productivity increases. As a result, macroinvertebrate community compositions transition in a continuum in response to the changing environmental conditions. Headwaters are typically nutrient limited, have cold water, and have abundant canopy cover that reduce the amount of sunlight that makes it to the river. This results in low primary production, low abundances of macroinvertebrates, and macroinvertebrate communities that are composed mostly of pollutant intolerant species. As you travel further from the headwaters and the river gets larger, more light reaches the substrate, more nutrients become available, and water temperatures increase. This results in more primary production, higher abundances of macroinvertebrates, and macroinvertebrate communities that are still dominated by pollutant intolerant species. As you continue further from the headwaters, the river become even more productive. There is an abundance of sunlight that reaches the substrate, water temperatures are warmer, there are even more nutrients available, and water velocity begins to slow. The increased primary production supports large abundances of macroinvertebrates but the warmer water and slower water velocity (and consequently finer sediment settling out of the water column) makes the habitat more suitable for pollutant tolerant macroinvertebrate species. The South Fork Snake River below Palisades Dam would likely fall into this transition zone of high productivity, warmer temperatures, and macroinvertebrate communities dominated by more pollutant tolerant species, if it were not for Palisades Dam.

Large reservoirs like Palisades Dam operate like a reset button in regards to the River Continuum. In general, large reservoirs slow water velocity, halt the transport of sediment, allow for stratification within the reservoir, and typically discharge cool, clear, and nutrient-poor water into the river below the dam. The cool, clear, and relatively nutrient-poor water, combined with a large order river that has abundant sunlight reaching the substrate and legacy nutrients from pre-dam conditions, makes for a productive system that contains high abundances of macroinvertebrates species that are both pollutant tolerant and intolerant. On the South Fork, the effect of the dam on macroinvertebrate compositions is most apparent directly below the dam where there are high abundances of EPT species but lower overall abundances of macroinvertebrates relative to the rest of the South Fork. The effects of Palisades Dam on macroinvertebrate compositions begins to fade with distance from the dam and that is evident by the increase in macroinvertebrate abundances and shift towards mostly pollutant tolerant species at the Lower SF site.

More than anything, this data provides critical baseline information about macroinvertebrate compositions and abundances on the South Fork. As we continue to sample every February, we will be able to monitor macroinvertebrate abundances and compositions over time and space to determine if macroinvertebrate communities are changing, and if so, what might be driving those changes.