Software applications for estimating micro-habitat conditions in natural channels (depth, velocities, channel indices) and the relative suitability of those conditions to aquatic life.
* flow regime
* physical habitat structure (channel form, substrate distribution, and riparian vegetation)
* water quality (including temperature)
* energy inputs from the watershed (sediments, nutrients, and organic matter)
http://www.fort.usgs.gov/Products/Software/PHABSIM/
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