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Scientific Investigations Report 2006-5025

Physical Habitat Classification and Instream Flow Modeling to Determine Habitat Availability During Low-Flow Periods, North Fork Shenandoah River, Virginia

Prepared in cooperation with the Northern Shenandoah Valley Regional Commission

By: J.L. Krstolic, D.C. Hayes, and P.M. Ruhl

This report is available as a pdf.


Increasing development and increasing water withdrawals for public, industrial, and agricultural water supply threaten to reduce streamflows in the Shenandoah River basin in Virginia. Water managers need more information to balance human water-supply needs with the daily streamflows necessary for maintaining the aquatic ecosystems. To meet the need for comprehensive information on hydrology, water supply, and instream-flow requirements of the Shenandoah River basin, the U.S. Geological Survey and the Northern Shenandoah Valley Regional Commission conducted a cooperative investigation of habitat availability during low-flow periods on the North Fork Shenandoah River. 

Historic streamflow data and empirical data on physical habitat, river hydraulics, fish community structure, and recreation were used to develop a physical habitat simulation model. Hydraulic measurements were made during low, medium, and high flows in six reaches at a total of 36 transects that included riffles, runs, and pools, and that had a variety of substrates and cover types. Habitat suitability criteria for fish were developed from detailed fish-community sampling and microhabitat observations. Fish were grouped into four guilds of species and life stages with similar habitat requirements. Simulated habitat was considered in the context of seasonal flow regimes to show the availability of flows that sustain suitable habitat during months when precipitation and streamflow are scarce. 

The North Fork Shenandoah River basin was divided into three management sections for analysis purposes: the upper section, middle section, and lower section. The months of July, August, and September were chosen to represent a low-flow period in the basin with low mean monthly flows, low precipitation, high temperatures, and high water withdrawals. Exceedance flows calculated from the combined data from these three months describe low-flow periods on the North Fork Shenandoah River. Long-term records from three streamflow-gaging stations were used to characterize the flow regime: North Fork Shenandoah River at Cootes Store, Va. (1925-2002), North Fork Shenandoah River at Mount Jackson, Va. (1943-2002), and North Fork Shenandoah River near Strasburg, Va. (1925-2002). 

The predominant mesohabitat types (14 percent riffle, 67.3 percent run, and 18.7 percent pool) were classified along the entire river (100 miles) to assist in the selection of reaches for hydraulic and fish community data collection. The upper section has predominantly particle substrate, ranging in size from sand to boulders, and the shortest habitat units. The middle section is a transitional section with increased bedrock substrate and habitat unit length. The lower section has predominantly bedrock substrate and the longest habitat units in the river. 

The model simulations show that weighted usable-habitat area in the upper management section is highest at flows higher than the 25-percent exceedance flow for July, August, and September. During these three months, total weighted usable-habitat area in this section is often less than the simulated maximum weighted usable-habitat area. Habitat area in the middle management section is highest at flows between the 25- and 75-percent exceedance flows for July, August, and September. In the middle section during these months, both the actual weighted usable-habitat area and the simulated maximum weighted usable-habitat area are associated with this flow range. Weighted usable-habitat area in the lower management section is highest at flows lower than the 75-percent exceedance flow for July, August, and September. In the lower section during these three months, some weighted usable-habitat area is available, but the normal range of flows does not include the simulated maximum weighted usable-habitat area.

A time-series habitat analysis associated with the historic streamflow, zero water withdrawals, and doubled water withdrawals was completed. During simulated historic drought periods, time-series habitat analysis shows weighted usable-habitat area to be limited for fast-generalist and pool-cover guilds in the upper management section, for fast-generalist and pool-run guilds in the middle section, and for the pool-cover guild in the lower section. The zero water-withdrawal scenario during historic low-flow periods shows improvement in weighted usable-habitat area for fast-generalist guild species in the upper management section and for pool-cover guild species in the lower section. The double water-withdrawal scenario simulation shows a total loss of fast-generalist guild weighted usable-habitat area during historic low-flow periods in the upper management section and a small decline in pool-cover guild weighted usable-habitat area in the lower management section. Simulated weighted usable-habitat areas are close to the maximum weighted usable-habitat area during a normal or wet historic summer period.

Streamflows that provide habitat at levels similar to those provided by the normal flow range (between the 25- and 75-percent exceedance flows) were identified for each management section of the North Fork Shenandoah River. With the current flow regime, the model results indicate that weighted usable-habitat area does not become highly limited for fish until streamflows reach or fall below the 90-percent exceedance flows for multiple days in July, August, and September. During low-flow periods, weighted usable-habitat area is limited in the upper section, in particular. Water conservation measures and reduced withdrawals may help maintain flows that sustain habitat in the upper section and throughout the river during low-flow periods.

Table of Contents



Purpose and Scope


Analysis of Historic Streamflow Data

Habitat Classification

Mesohabitat Classification



Hydraulic Data Collection in the Predominant Mesohabitat Types

Selection of Reaches

Description of Reaches and Transects

Hydraulic Data Collection Methods

Fish-Community Sampling and Microhabitat Observations

Community Sampling

Microhabitat Observations

Development of Fish Habitat-Suitability Curves

Canoeing Suitability Curves

Instream Flow Modeling to Determine Fish Habitat Availability

Model Calibration


Water-Surface Elevation Calibration

Velocity Calibration

Habitat Simulation and Development of Weighted Usable-Habitat Area Curves

Habitat-Discharge Relations for the ManagementSections 

Upper Section

Middle Section

Lower Section

Time-Series Analysis for Low-Flow Periods

Summary and Conclusions


References Cited

Appendix 1. RHABSIM Model-Calibration Data from the Hydraulic
Data-Collection Reaches

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