Hydroecological Integrity assessment Process (HIP)

Software applications for conducting a hydrologic classification of streams, addressing instream flow needs, and assessing past and proposed hydrologic alterations on streamflow and/or other ecosystem components.

http://www.fort.usgs.gov/Resources/Research_Briefs/HIP.asp

Physical Habitat Simulation (PHABSIM) Software

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/