There are four major components of a stream system that determine the productivity of the fishery (Karr and Dudley 1978). These are: (1) flow regime, (2) physical habitat structure (channel form, substrate distribution, and riparian vegetation), (3) water quality (including temperature), and (4) energy inputs from the watershed (sediments, nutrients, and organic matter). The complex interaction of these components determines the primary production, secondary production, and fish population of the stream reach.

The basic components and interactions needed to simulate fish populations as a function of management alternatives are illustrated in Figure I.1. The assessment process utilizes a hierarchical and modular approach combined with computer simulation techniques. The modular components represent the "building blocks" for the simulation. The quality of the physical habitat is a function of flow and, therefore, varies in quality and quantity over the range of the flow regime. The conceptual framework of the Incremental Methodology and guidelines for its application are described in "A Guide to Stream Habitat Analysis Using the Instream Flow Incremental Methodology" (Bovee 1982).

Simulation of physical habitat is accomplished using the physical structure of the stream and streamflow. The modification of physical habitat by temperature and water quality is analyzed separately from physical habitat simulation. Temperature in a stream varies with the seasons, local meteorological conditions, stream network configuration, and the flow regime; thus, the temperature influences on habitat must be analysed on a stream system basis. Water quality under natural conditions is strongly influenced by climate and the geological materials, with the result that there is considerable natural variation in water quality. When we add the activities of man, the possible range of water quality possibilities becomes rather large. Consequently, water quality must also be analysed on a stream system basis. Such analysis is outside the scope of this manual, which concentrates on simulation of physical habitat based on depth, velocity, and a channel index.

The results form PHABSIM can be used alone or by using a series of habitat time series programs that have been developed to generate monthly or daily habitat time series from the Weighted Usable Area versus streamflow table resulting from the habitat simulation programs and streamflow time series data. Monthly and daily streamflow time series may be obtained from USGS gages near the study site or as the output of river system management models.