This analysis of relative aquatic habitat integrity in the Lower/Middle Klamath and the Upper Sacramento, was requested by World Wildlife Fund to inform the comprehensive conservation plan being pursued in the Klamath-Siskiyou Terrestrial Ecoregion. This plan is based on David Brower’s concept of planetary CPR (Conservation, Protection, Restoration), and aims to: conserve, protect and restore the Klamath-Siskiyou ecoregion in harmony with local communities. Through this plan, regional conservation planning has focused on three broad (ecoregion wide) conservation goals: 1) Conservation of 5-10% of the 1,416,450 hectares (3.5 million acres) of private lands through conservation easements, fee-title acquisitions, and market-based solutions; 2) Protection of 30-40% of the 2,630,550 hectares (6.5 million acres) of public lands; and 3) Restoration of focal species (e.g., salmon) and keystone ecosytem processess (e.g. fire).