The BioNet Reference Codex contains documentation and helpful descriptions of various aspects of the biological assessment program.
Topics of Interest:
BMIBI - Benthic Macroinvertebrate Index of Biotic Integrity
FHI - Fish Habitat Index
FIBI - Fish Index of Biotic Integrity
QAQC - Quality Assurance/Quality Control
StreamStats - A USGS web application that can be used to determine drainage areas, basin GIS, and many other features.