Habitat fragmentation, the process by which contiguous native vegetation is subdivided into smaller, more isolated patches, impacts species directly through habitat loss. There may also be indirect effects on species' populations, such as reduced reproductive success or increased predation risk. The ABMI measures habitat fragmentation by calculating effective mesh size, which incorporates the size of native vegetation patches and proximity to human footprint. Larger mesh size values occur in bigger native vegetation patches further away from human footprint, whereas smaller mesh size values indicate smaller patches and more human footprint. 

The primary source of data when creating the Effective Mesh Size layers was the 2012 Wall-to-wall Human Footprint Inventory. All areas that were not classified as human footprint were assumed to be native vegetation, and mesh size was calculated based on these polygons. Because linear footprint can dramatically influence effective mesh size, mesh size was calculated in two ways—counting linear features as human footprint that separates native patches, and not counting linear features as human footprint that separates native patches.