Section 7 of the Endangered Species Act requires that any federal agency proposing to do anything – issue a permit to someone else, spend its money on a project, take a direct action – that might affect an ESA-listed species must first consult with NOAA Fisheries Service about such effects. The involved federal agency (action agency) must send a description of its intended action to the fisheries service in what’s called a biological assessment. A BA outlines what the agency believes the biological consequences of its action will be.

NOAA Fisheries Service usually consults with the other agency on the
proposal and formally responds with a biological opinion. The primary goal of
a BiOp is to ensure that a listed species isn't put in jeopardy; that is, put at risk of extinction, by the federal action. Although the document is called an “opinion,” it actually has the force of a decision document: the federal
agency whose actions it governs must comply with it. A BO is purely biological; it’s a scientific judgment about a proposed action, not a policy document.

If what’s being proposed to NOAA Fisheries Service isn't likely to put listed species in jeopardy, then a “no-jeopardy” BiOp is issued, giving the other agency the green light for its proposed action. If the proposed action is likely to result in unacceptable harm to listed fish, NOAA Fisheries Service issues what’s called a jeopardy opinion. A jeopardy opinion always has reasonable and prudent measures required to minimize any harmful effects on the listed species.

A biological opinion therefore can include conservation recommendations to minimize or avoid possible adverse effects on listed species or their critical habitat. It can also impose reasonable and prudent measures necessary to minimize any harmful impacts, and can require monitoring and reporting to ensure adequate species-protection compliance. The bottom line: a BiOp prevents unacceptable harm to a listed species or its habitat.

A biological opinion is not an Endangered Species Act recovery plan, but can be a component of such a plan, and is one part of the ESA process.

Some ESA Section 7 consultations can be completed informally, without issuance of a biological opinion. Actions considered not likely to adversely affect listed fish are submitted to NOAA Fisheries Service for informal consultation and concurrence.