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South Fork Snake River Macroinvertebrate Study, 2020 & 2021

Updated: Jan 13, 2022


  • 2021 is our third year of long-term monitoring of aquatic macroinvertebrates (insects and other creatures that live in the river bottom) in the South Fork Snake River at Upper South Fork, Canyon South Fork, and Lower South Fork locations.

  • Mean total abundance of macroinvertebrates declined by ~100,000 individuals/meter (~65%) for the Canyon South Fork and Lower South Fork locations from 2019 to 2021, but remained the same for the Upper South Fork location. The decline at the Canyon South Fork and Lower South Fork was largely a product of significant declines in abundances of midges and non-insects.

  • HBI index scores (index that uses macroinvertebrate abundances & diversity to qualify habitat) and percent EPT (percent mayfly, stoneflies, and caddisflies) improved for the Canyon South Fork and Lower South Fork locations, indicating improvements in aquatic habitat conditions.

  • One immature New Zealand Mud Snail (NZMS) was found in a 2021 Canyon South Fork sample. While not the first NZMS found in Idaho, nor the South Fork Snake River, finding an invasive species in one of our samples highlights the importance that anglers and river users need to be diligent about following best practices when it comes to aquatic invasive species. Clean, drain, and dry your equipment!

I apologize it has taken me a year to report on 2020 South Fork data. Last year was a busy year and the HFF-SFI program continued to operate at full speed all while navigating the trials and challenges of a global pandemic. For future years, we are hoping to get our spring data back from the lab by early June so we can report on aquatic macroinvertebrate abundances and compositions prior to summer for the same year the samples were collected. Additionally, we haven’t received the 2021 Henry’s Fork macroinvertebrate data back yet but I will be writing another blog highlighting the Henry’s Fork data as soon as we do.

Below is copy and pasted background information on the who, what, when, where, why, and how we collect data on aquatic macroinvertebrates (Thanks, Dr. Van Kirk!). If you want to skip straight to the results, scroll to the bottom.

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 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 years 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 is new on the South Fork?


Mean total abundance of macroinvertebrates at the Canyon South Fork and Lower South Fork locations declined by ~100,000 individuals/meter (~65%), and the decline in total abundance was statistically significant at the Lower South Fork location (Figure 1). Total abundance of macroinvertebrates at the Upper South Fork had no statistically significant change in total abundance between 2019 to 2021 but had the highest abundances of macroinvertebrates out of the three locations in 2021 (~100,000 individuals/meter).

In 2019, the Lower South Fork and Canyon South Fork had nearly three times the number of macroinvertebrates as the Henry’s Fork but in 2020 and 2021, macroinvertebrate abundances at these two locations declined and are now comparable to abundances of macroinvertebrates at the Upper South Fork and the Henry’s Fork sites (~30,000 - 50,000 individuals/square meter). This decline was largely a result of declines in midges and non-insects (snails, worms, etc.) at the two locations. The Upper South Fork site didn’t show any statistically changes in total abundance from 2019 to 2021 and currently has the highest abundances of macroinvertebrates out of South Fork and Henry’s Fork locations.


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.

Shannon’s diversity index scores across all South Fork sites showed little change from 2019-2021, and none of the changes were statistically significant. Shannon’s diversity index scores ranged between 2.3-2.8 for South Fork locations which is relatively high for aquatic macroinvertebrate communities and is comparable to scores for Henry’s Fork locations.

Hilsenhoff 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) indicate more degraded aquatic habitat conditions. Conversely, lower HBI scores (higher abundances of species with lower tolerance to habitat degradation) indicate better aquatic habitat conditions. Click here for a complete description of HBI.

HBI scores fluctuated between 2019 to 2021 but in general, HBI improved or stayed consistent for all three sites and South Fork habitats range from “Fair” to “Excellent” quality. The Upper South Fork location had a statistically significant decrease in HBI (improvement in habitat) from 2019 to 2020, but the small increase in HBI between 2020 and 2021 was not statistically significant. HBI for the Canyon South Fork location showed statistically significant improvements since 2019, elevating habitat classification from “Fair” to “Excellent”. Additionally, HBI for the Lower South Fork location also showed statistically significant improvements since 2019 with habitat classification going from “Fairly poor” to “Fair”.

Percent EPT (mayflies, stoneflies, and caddisflies)

Percent EPT is the percent of the individuals at the site that are mayflies (Ephemeroptera), stoneflies (Plecoptera), and caddisflies (Trichoptera). From 2019 to 2021, there wasn’t a statistically significant change in percent EPT at the Upper South Fork location, while the Canyon South Fork and Lower South Fork locations had statistically significant increases in percent EPT. The mean percent EPT for the Canyon South Fork site roughly tripled and the Lower South Fork site doubled from 2019 to 2021.


At face value, the decline in total abundance of macroinvertebrates at the Canyon South Fork and Lower South Fork may seem extreme but when put into context with macroinvertebrate abundances relative to other river systems and after identifying what species of macroinvertebrates declined, the South Fork still has very high abundances of critical, pollutant-intolerant species (e.g. mayflies, caddisflies, and stoneflies). The decline in total abundances was in large part due to declines in more pollutant-tolerant species (midges and non-insects). This shift in macroinvertebrate compositions is indicative of improvements in aquatic habitat conditions which was captured both in the improvement in HBI scores and percent EPT.

What led to the improvements in aquatic habitat conditions at the Canyon South Fork and Lower South Fork? We don’t exactly know. Three years of data might sound like a lot but it isn’t enough to develop biologically sound hypotheses to test with statistical methods with any power. A whole host of variables could impact macroinvertebrate abundances (i.e. water temperatures, flows during various times of the year, flow adjustments, nutrients, periphyton, etc.) and it could take several more years before we have enough data to begin understand the how these variables may or may not be impacting macroinvertebrate abundances and compositions in the South Fork. That being said, understanding these relationships will be critical in developing strategies to present to state and federal partners that aim at protecting and improving aquatic macroinvertebrates and habitat based on solid data and research. This is a core reason why we continue this long-term monitoring effort.

While our macroinvertebrate monitoring study design isn’t focused on finding or monitoring rare or invasive species, Brett’s lab does a full sample scan for rare, threatened, or endangered species and reports this data. In one of the 2021 Canyon South Fork samples, an immature New Zealand Mud Snail (Potamopyrgus antipodarum) was found in the sample. New Zealand Mud Snails (NZMS) are an invasive species that are thought to be first introduced in the Snake River (and the USA) near Hagerman area in the late 1980s, likely through overseas fish trade for aquaculture programs. Since the 1980s, NZMS have found their way into 21 other states and various watersheds within these states (USGS, NZMS). In Idaho, NZMS have been found in the Snake River, Salmon River, Boise River, Silver Creek, and various other waterbodies in Idaho. The last reported sighting of a NZMS in the South Fork was near the confluence of Fall Creek and the South Fork in 2015 (IDFG observation reporting). While NZMS can have significant impacts on native aquatic macroinvertebrates communities via interspecies competition for resources, it is difficult to predict their impacts on localized aquatic macroinvertebrate communities. Seeing that NZMS have been in the South Fork Snake River since as early as 2015 and there hasn’t been an apparent spread or increase in their abundance in the system, it seems unlikely that finding this NZMS is indicative of a major expansion and increase in abundance that would lead to significant native aquatic macroinvertebrate impacts. Due to the lack of NZMS sightings anywhere else in the South Fork, expert entomologist I have contacted suspect it is likely that the NZMS found in the Canyon South Fork sampling location got to the location through human-assisted transport. Even though we don’t know for sure how NZMS got in the Canyon South Fork reach, nor do we know if NZMS will impact macroinvertebrate communities in the Canyon South Fork, our annual sampling will allow us to monitor NZMS presence and abundances at the location.

The presence of a NZMS in one of our samples underlines a crucially important point; all anglers and river users should be practicing proper aquatic invasive species etiquette, particularly when traveling between waterbodies. Please be diligent about cleaning, draining, and drying all your equipment when traveling between waterbodies! Even though the NZMS may or may not have a significant impact on native aquatic macroinvertebrate compositions in the South Fork, all invasive species have the potential to cause significant and irreversible impacts on native species communities. So again, please clean, drain, and dry your equipment to keep the iconic South Fork macroinvertebrates healthy and abundant!



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