The Framework Matrix is organized according to three levels of ecological analysis that could be considered for each of six adaptation objectives. This is based on the consensus that "climate-adaptive" conservation plans should not only be geared toward conserving species and their habitats, but also should ensure that ecological and evolutionary processes can continue to operate across landscapes over the coming decades of climate change. By contrast, most assessments that inform planning today continue to focus somewhat more narrowly on current and/or future species assessments.

Ideally, assessments should be conducted for all three levels of analysis in order to be ecologically complete. However, this may not be feasible because of limitations imposed by available data or cost, or may not be desired because of stakeholder values and planning information needs. Nevertheless, it is recommended that assessments that focus on one level of analysis at least be placed into the context of the next higher level. For example, planners may only wish to understand the fate of focal species (e.g., desert tortoise, prairie chickens, sage grouse, pikas) under climate change. But considering the community context for these species' distributions (e.g. the species' food and habitat) would strengthen the species level assessment by providing insights about the fate of important resources supporting the species. Regardless, the approaches, tools, and data used to conduct assessments will differ between the levels of ecological analysis.

The ecological analysis levels are:

A. Landscape level

B. Ecosystem level

C. Species and populations