Under the Endangered Species Act, a federal agency whose proposed actions may affect a listed species (or its habitat) must assess the potential impacts of its actions in a document called a biological assessment or BA.

As part of the remand of the 2004 FCRPS Biological Opinion the action agencies submitted a BA and a comprehensive analysis to NOAA Fisheries on August 21, 2007.

The comprehensive analysis responded to a ruling by Judge Redden in the remand of the Upper Snake BiOp. Judge Redden ruled that the analysis of effects in the 2004 FCRPS BiOp remand be integrated with the analysis of effects for the Upper Snake River BiOp remand, resulting in a "comprehensive analysis" of the effects of the two actions on the listed species and designated critical habitat. This is a thorough lifecycle survival analysis that looks at the status of each of the listed stocks and the factors that have contributed to their decline, assesses the impact of the federal agencies proposed actions and makes a determination of whether those actions and the actions of others will contribute to the recovery of these fish.

The BA built on the action agencies' Proposed Action, submitted to NOAA Fisheries in May of 2007, containing more than 70 specific actions in the areas of hydropower system improvements, hatchery reforms and habitat enhancements. Together, these described how federal actions in the hydropower system would assure survival and provide for recovery of threatened and endangered fish stocks through a collaborative effort among states and tribes.

NOAA Fisheries will use these documents to do an independent analysis and develop new BiOps for the operation of these dams for listed fish.