The Framework Matrix is built around the consideration of six major adaptation objectives for biodiversity conservation and climate adaptation. Assessments frequently focus on a subset of the adaptation objectives. Users of the framework are encouraged to assess as many of the adaptation objectives and levels of ecological analysis as is feasible based on their planning context and the resources available.

The choice of adaptation objectives should be steered by the biological characteristics of the species of concern. For example, one may choose to conduct assessments that support the maintenance or restoration of ecological connectivity if one is dealing with species that are expected to undergo major shifts in geographic range in response to climate change (Adaptation Objective 6). One may choose to conduct assessments that identify parcels of land within a watershed or along a seacoast that will support biodiversity in the future as sea-level rises (Adaptation Objective 4).

As a matter of sound practice, any assessment should be systematically motivated by a clear understanding and articulation of the conservation problem and associated ecological conditions before choosing the analysis approaches, tools, and data for the assessment. That is, let the conservation issue define what approaches, tools, and data are needed for the assessment. Oftentimes, assessments are driven by availability of data and tools rather than by clear problem definition, which can lead to assessment outcomes that will fail to meet the needs of planners.

The adaptation objectives are:

1. Protect current patterns of biodiversity.
2. Protect large, intact, natural landscapes and ecological processes.
3. Protect the geophysical setting.
4. Identify and manage areas that will provide future climate space.
5. Identify and protect climate refugia.
6. Maintain and restore ecological connectivity.