First Advisor

Yangdong Pan

Term of Graduation

Spring 2021

Date of Publication


Document Type


Degree Name

Master of Science (M.S.) in Environmental Science and Management


Environmental Science and Management





Physical Description

1 online resource (x, 119 pages)


Fine sediment (particles < 2 mm in diameter) deposition is a natural component of streams but in excess amounts it is harmful to aquatic biota. Fine sediment is the main cause of impairment in streams and rivers of the Pacific Northwest and it can lead to unsuitable spawning and rearing habitat for Endangered Species Act (ESA) listed Salmon and steelhead. From a regulatory perspective, fine sediment presents a challenge because it is difficult to measure in situ and to establish criteria that would indicate stream impairment. Consequently, there is considerable effort to develop biocriteria using stream macroinvertebrates that would help regulators determine if a stream is impaired by excessive fine sediment. Stream macroinvertebrates are widely used to monitor and assess stream degradation because they are affected by the physical, chemical and biological conditions in a stream. In particular, the stream insects known as mayflies (Ephemeroptera, E), stoneflies (Plecoptera, P) and caddisflies (Trichoptera, T) are commonly used as a metric referred to as EPT richness. EPT taxa are well known as pollutant intolerant insects and EPT richness in known to respond negatively to stream degradation. While the sensitivity of EPT to changing water chemistry, increased land use, and hydrologic alteration has been well established, the use of EPT as biocriteria to monitor fine sediment conditions in streams has not been fully evaluated. Studies on the relationship between EPT and fine sediment have shown mixed results, which is likely due to the challenges of quantifying fine sediment in streams. For example, many studies use reach-scale pebble-counts to quantify sediments and reach-scale macroinvertebrate samples to characterize their condition, but the processes that drive macroinvertebrate-sediment relationships primarily operate at the patch-scale. Another issue is the incomplete sediment gradient often observed in the randomized, reach-scale study designs frequently used to collect stream data for regulatory purposes. The purpose of my thesis is to address the use of stream macroinvertebrates as indicators of excessive fine sediment in the regulatory setting. Specifically, I evaluated which aspect of the macroinvertebrate community should be used as an indicator for fine sediment, explored methods for better characterizing benthic fine sediment at the patch-scale and conducted a spatially oriented study that contained a fine sediment gradient. I accomplished this by: 1) using Random Forest and generalized linear models (GLM) to explore relationships between environmental variables, macroinvertebrate metrics and fine sediment in the Pacific Northwest (PNW), 2) developing and validating a novel methodology that quantifies macroinvertebrates and fine sediment at the patch-scale, and 3) designing and conducting a field study in the John Day Basin that included a relatively complete gradient of fine sediment conditions. The results of the exploratory analysis of the PNW data showed that EPT richness and percent EPT richness had the strongest association with fine sediment (model percent variance explained = 42.6% -- 44.5%). Important environmental predictors of EPT richness included percent fine sediment cover, conductivity, chloride, canopy cover and fast-water habitat. Generalized linear models with EPT richness as the response variable and the same environmental predictor variables showed similar results (Pseudo R2 = 0.43 -- 0.50). Using the novel patch-scale sediment sampling methodology, I found that mass of fines and percent of fines was significantly and negatively correlated with velocity (rho = - 0.78, p < 0.001 and rho = -0.52, p < 0.05, respectively). Percent EPT richness exhibited significant and positive correlations with velocity (rho = 0.87, p < 0.001) and a significant and negative correlation with mass of fines (rho = - 0.70, p < 0.01). Non-erosional samples exhibited stronger relationships between velocity and mass of fines (rho = -0.85, p < 0.01) than erosional sampling locations (rho = 0.20, p > 0.05). Results of the John Day study showed that EPT richness was strongly related to fine sediment mass and also positively related to orthophosphate (Pseudo R2 = 0.82). EPT richness decreased 12% between zero and seven percent fine sediment cover but increased between 8% and 10% fine sediment cover. When compared to data collected using a traditional reach-scale approach, the John Day study resulted in stronger relationships between stream macroinvertebrates and fine sediment, and improved model R2 values by 52%. These findings provide support for the conceptual premise that 1) EPT richness may be a useful indicator for excessive fine sediment conditions, 2) characterizing sediment and macroinvertebrates at the patch-scale and along non-erosional habitats results in better statistical relationships, and 3) a study design that is specifically focused on the fine sediment gradient resulted in better statistical models than the traditional reach-scale approach typically used in the regulatory setting. The results of this study have several limitations that are important to acknowledge. First, the coefficients of the GLM models should not be used in basins other than John Day. Second, the novel patch-scale sediment sampling method is probably too time consuming for use in regulatory monitoring; however, its use to develop macroinvertebrate indicators of fine sediment would likely improve the ability to detect excessive fine sediment conditions. And finally, because EPT richness is known to vary with other environment stressors, caution should be exercised when applying this approach in basins with other environmental stressors. Further research assessing how EPT traits decline in response to fine sediment could help distinguish between changes due to excessive fine sediment and other stressors.


© Cory Michael McCaffrey

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