As discussed in the summary of the ESA, a non-federal entity (such as a business, landowner or government) may incidentally "take" (harm) a listed species through an approved Habitat Conservation Plan (HCP). In an HCP, a set of actions that protect and benefit a listed species serve as mitigation for takes of that species that are incidental to otherwise lawful activities, such as harvesting trees, constructing roads or permitting development. Through an approved HCP, the applicant receives legal assurance that it can conduct its business without disruption by regulatory action under the ESA. In return, the federal government receives assurance that protection of the species occurs on a more sustained, systematic and cost-effective basis than is possible through individual consultations and enforcement actions under the ESA. HCPs have become widespread, particularly under the Clinton administration, since they were created as an option for non-federal entities in 1982.

HCPs are approved based on the following criteria:

• Impacts on habitat are minimized and mitigated to the maximum extent practicable;
• The applicant has adequate authority and funding to implement the plan;
• The approved take "will not appreciably reduce the likelihood of survival" of the species; and
• Other criteria determined by the responsible federal agency, which may include consistency with a recovery plan for the species developed by the agency; this would have a goal of reversing the endangered or threatened status of the species, rather than merely not reducing the likelihood of its survival. (NMFS is unlikely to have completed such a plan for Puget Sound Chinook for several years.)

Between the time the final listing decision is made and an incidental take permit is issued, the applicant is fully bound by the ESA: all actions that might "take" a listed species are subject to federal consultation and regulatory action under Section 7 of the ESA; they are also subject to third party lawsuits seeking such action. However, if the responsible federal agency believes that an applicant is pursuing an HCP in good faith, it may choose to be lenient in applying regulatory restrictions during this period, though it is not required to do so.

Multi-species HCPs, which typically address whole ecosystems (such as watersheds) are encouraged by the federal government and provide advantages to applicants. They allow for the incidental take of all species for which they are approved—including species that may not have been listed at the time the permit is issued.

Some lessons learned from HCPs that have been approved or are under development include:

• Satisfactory HCPs are expensive and time-consuming to develop and are typically even more expensive to implement (a multi-species HCP in San Diego County has taken more than seven years to develop and will cost more than $400 million over 20 years to implement);
• Key stakeholders must participate in the development of an HCP to ensure their support when the HCP is being considered for approval;
• HCPs must be guided by the best independent science available;
• A strong yet flexible central administration is critical to development of an acceptable HCP;
• HCPs should have a long-term outlook but provide opportunities for incremental action.