Madison River Foundation

Baseline Macroinvertebrate Monitoring Report fall 2016-fall 2017 Upper Madison River & Northwestern Energy Madison and Missouri River Macroinvertebrate Biomonitoring 2016 and 2017 Data Summary


The Madison River Foundation contracted Montana Biological Survey to conduct an upper Madison River baseline macroinvertebrate monitoring program in the fall of 2016. This study was initiated to supplement and augment the existing Northwestern Energy monitoring program.

NorthWestern Energy conducts quarterly monitoring of 30 different water quality parameters at four different locations along the Madison River in a program that has been ongoing since 1995. Aquatic insect populations are also monitored annually at four river stations each summer.

The Foundation elected to fund seasonal samplings in order to monitor macroinvertebrate population or taxa trends that may go unnoticed when sampling occurs only once in the middle of summer. In addition, the MRF study established two sites closer to Hebgen Dam than Northwestern Energy’s site, which lies downstream of Cabin Creek.

The project goals for MRF’s program:

1) To conduct standardized and quantitative macroinvertebrate surveys to serve as baseline standards for future monitoring efforts within this Madison River section.

2) To establish seasonal macroinvertebrate population estimates and community characteristics to assess aquatic bio-integrity.

3) To understand the macroinvertebrate dynamics in relation to Hebgen Dam’s retrofits and differential temperature flow patterns.

This report serves as a comparative summary of the results of the Baseline Monitoring Macroinvertebrate Report 2016-2017 for the Upper Madison River prepared by David Stagliano, Aquatic Ecologist through Montana Biological Survey and Northwestern Energy’s data summary in 2017 for annual macroinvertebrate monitoring. The macroinvertebrate report for sampling from fall 2016 through fall of 2017 was received by MRF from David Stagliano in December 2018.


In September 2016, May 2017 and October 2017 Montana Biological Survey collected quantitative, replicated macroinvertebrate samples, habitat data and water chemistry measurements at eight Madison River sites.

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Three replicate Hess (33 cm diameter)  dip-net samples were taken at each site to collect macroinvertebrates within a designated riffle at measured distances from the bank. Hess samples are considered more quantitative than the dip-net samples and were chosen if substrate sizes allowed. Three Hess samples typically capture 90% of the total taxa present in a riffle. Two additional Hess or dip-net samples were taken adjacent to the original benthic sites and checked for salmonfly nymphs, which were recorded on data sheets and released.

NorthWestern Energy conducts their monitoring in the summer typically between July-August at 11 sites.

NorthWestern Energy Sampling Sites:

  1. Madison River in Yellowstone National Park (YNP) near USGS 6-375

  2. Madison River 2 km below Hebgen Dam ~ 1 km below USGS #6-385

  3. Madison River at Kirby Ranch

  4. Madison River at Ennis Campground

  5. Madison River below Madison Powerhouse at USGS gauge 6-410 (Ennis Reservoir)

  6. Madison River above Norris Bridge

  7. Madison River at Greycliff Fishing Access

  8. Missouri River at Toston near USGS gage 6-545,

  9. Missouri River about 100 m. below Hauser Dam - east bank

  10. Missouri River about 1 km below Holter Dam –west bank

  11. Missouri River about 100 m. below Morony Dam

The modified kick-net procedure is employed to obtain five samples per site. A sampling grid is placed on the stream bottom in a selected habitat type. A large rectangular net was held immediately downstream from the grid. Cobbles were hand scrubbed and smaller sediments were vigorously stirred by foot. The contents of the net (macroinvertebrates, vegetation, sediment, and debris) were preserved in 90% ETOH.


MRF Study Results Summarized:

Overall, 108 unique macroinvertebrate taxa were reported from the 96 seasonal macroinvertebrate assessment samples collected between Hebgen Dam and Ennis in 2016-2017. Densities of benthic macroinvertebrates varied significantly spatially and seasonally with the overall trend of higher densities from HWY 87 Bridge and decreasing downstream to Varney then increasing densities at Ennis. The Madison River at the HWY 87 Bridge reported the highest benthic invertebrate densities of all sites in the fall, but then significantly decreased in the spring. Relatively high average densities were reported across all sites, which trended slightly higher in the spring 2017 samples. Overall seasonal trends across the sites are decreases in the summer invertebrate densities. We observed lower than average densities at both Madison River Hebgen sites and at the Varney Bridge site. Lower macroinvertebrate population densities did not necessarily equate to lower taxa richness, as Varney Bridge reported the lowest densities, but also had the 2nd highest taxa richness and EPT (Mayfly, stonefly, and caddisfly) richness in the spring. Salmonflies gradually increased their densities from their lowest numbers below Hebgen Dam site #2 to peak density at Varney Bridge; this is a sevenfold increase. Lower than average salmonfly numbers are also reported near Ennis, at McAtee Bridge and HWY 87 Bridge, especially in the spring.

In addition, New Zealand mudsnails have persisted in low densities at multiple sites in the Madison River from Yellowstone Park to Ennis, since their peak abundances were reported in 2003. They appear to be substantially increasing their populations downstream of Hebgen Dam at the MRF sites; three times higher than the data collected from the NWE “Hebgen” site. We postulate that NZMS population increases, overall decreased biological integrity and mayfly, stonefly and caddisfly decreases directly below Hebgen Dam is correlated with lower than average spring flushing flows and the previous years’ warmer water temperature releases from the dam. We conclude that cold-water input from the tributary, Cabin Creek, is significantly improving the health of the macroinvertebrate community at the NWE monitoring site compared to those upstream from its confluence. In general, most biological integrity metrics reflect increases in macroinvertebrate health in proportion to the site’s distance from Hebgen Dam.

NorthWestern Energy Results Summarized:

Community composition varied throughout the drainage with six major taxonomic groups accounting for most of the benthos. Dipterans, caddisflies, mayflies, and non-insects were present at all sites while beetles and stoneflies had more limited distributions. Mayflies were present throughout the drainage, attaining greatest relative abundance in the Madison River at Hebgen, Norris, and Greycliff. Caddisflies were also widely distributed and were numerically dominant at two Madison River sites (YNP and ENN). Stoneflies were common in the upper Madison River but were mostly absent downstream from Ennis Reservoir. Blackflies (Diptera) and sowbugs (noninsect-crustaceans) were extremely abundant below Ennis. Snails were abundant in the Madison River below Hebgen Reservoir and at Kirby and were generally distributed throughout the system.

The 2016 bio-integrity scores ranged from 43% to 93%, with the highest score at Ennis and the lowest scores at the Madison Powerhouse. The most recent assessment indicated improved environmental conditions during 2016 in the upper Madison River from Hebgen to Ennis. Bio-integrity estimates were relatively high (~ near or above 80%) for all Madison River sites except at the Madison Powerhouse.

Characterization of macroinvertebrate assemblages based on temperature tolerance showed a clear dichotomy between the upper and lower reaches of the Madison River. Coldwater taxa were more abundant in the upper river while warm water taxa predominated in the lower river. The influence of the thermal regime on community composition was evident below Hebgen Reservoir. Changes in the relative abundances of cold-water and warm-water macroinvertebrates were evident during the past nine years. Normally (i.e. 2008 and 2016), the dam releases colder hypolimnetic water during the summer. However, due to construction at the dam, warmer surface water was released from 2009 through 2016. Community responses to changes in the thermal regime appear to be cumulative over several years.


The updated Baseline Monitoring Report included information on results of a full year of sampling on the Upper Madison River 2016 through 2017. The study was conducted during the Hebgen Dam retrofit and effectively monitored changes throughout the project. The retrofit completion between 2016 and 2017 in conjunction with higher average stream flows in 2017, appears to have improved the macroinvertebrate community’s optimal and maximum thermal limits, as well as the bioassessment scores and taxa metrics since sampling began in fall of 2016. It is very difficult to evaluate dam retrofit effects at the long-term NWE monitoring site due to the mediating effects of Cabin Creek, but the two MRF sites provide multiple lines of macroinvertebrate evidence to support this conclusion.