HABITAT SUITABILITY ANALYSIS USING HYDRAULIC PARAMETERS FOR THE ENDANGERED HIGGINS’ EYE PEARLYMUSSEL IN POOL 16 OF THE UPPER MISSISSIPPI RIVER

Author

• Holly Marie Chesney, Southern Illinois University CarbondaleFollow

Date of Award

8-1-2026

Degree Name

Master of Science

Department

Geography and Environmental Resources

First Advisor

Remo, Jonathan

Abstract

Degradation of riverine habitat and water quality caused by river engineering, urban development, and industrial agriculture has led to many freshwater mussel species (Unionidae) being designated as species of concern by state and federal agencies. The Higgins’ eye pearlymussel (Lampsilis higginsii) is a federally listed endangered species that historically occupied the Upper Mississippi River (UMR; upstream of the Missouri River confluence).The UMR was extensively modified during the 1930s through the construction of a series of low-head dams to support commercial navigation. These structures created a sequence of navigation pools and established a 2.7 meter- depth navigation channel to facilitate commercial barge traffic. Maintaining this channel requires routine dredging, which disturbs the benthic environment and has been identified as a primary stressor affecting aquatic habitats along the UMR. Dredging activities can directly disrupt mussel beds by removing or burying individuals, altering substrate composition, and degrading habitat conditions essential for survival and reproduction. Despite these ongoing disturbances, the Higgins’ eye persists in some segments of the UMR. However, the extent to which channel maintenance dredging contributes to impacts on mussel populations remains insufficiently quantified, representing a critical gap that this study seeks to address. This study focuses on identifying and quantifying suitable habitat for large freshwater mussel species within the UMR’s Pool 16 using hydraulic and hydrologic variables that have been identified as important predictors of mussel habitat (i.e., frequency and magnitude of suitable shear stresses or flow velocities). The hydraulic variables are quantified using a 2D hydrodynamic model developed in HEC-RAS using a high-resolution topographic and bathymetric elevation model. Model predictions were calibrated and validated using three longitudinal water surface elevation surveys along with other observed hydrologic data. Using this model derived, hydraulic variables, and mussel survey data; a habitat suitability analysis was undertaken. The suitability analyses were validated using mussel survey data collected in Pool 16 from 2019 to 2024. Results showed that shear stress values between 0.48 and 2.9 N/m² were most favorable for large mussel species, consistent with theoretical and analytical thresholds. Approximately 85% of surveyed mussels occurred in areas that remained inundated and experienced shear stress within this range at least 20% of the time, indicating a preference for locations with moderate flows capable of flushing fine grained sediments from mussel beds at least annually. Suitable velocity ranges derived from the literature (0.3–1.0 m/s) were also evaluated, and mussels were found to occupy areas within this range at least 50% of the time, primarily under moderate to low flow conditions (40–90% daily exceedance probability). However, shear stress was ultimately selected as the primary habitat suitability metric because it more directly reflects substrate stability and near bed hydraulic conditions than modeled depth averaged velocity. These findings have direct implications for navigational and environmental management by identifying areas where mussel habitat is more likely to occur. Habitat suitability analyses can be used to support management decisions regarding dredge spoil placement by helping managers minimize hazardous impacts to areas that are likely to support mussel habitat. This approach can assist in balancing navigational needs with the protection of endangered species.