Habitat loss is the largest threat to bat populations globally and the greatest threat faced by the three Connecticut tree-roosting bat species (silver-haired bat, eastern red bat, and hoary bat). While not currently the primary threat to Connecticut cave bats, habitat loss still adds to the pressure faced by these species. 

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Habitat loss in Connecticut is both direct and indirect. Direct losses come from deforestation and fragmentation caused by timber harvest, land development, and quarrying, to name a few. Indirect loss comes from habitat degradation resulting from irresponsible tourism. An example of this would be people entering caves or abandoned mines used by bats for hibernation. This activity has a similar effect as white-nose syndrome, because it leads to the disturbance of the bats and forces them to use up their critical stored resources. 

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All bat species in Connecticut rely on forests in some form (for foraging, roosting, and/or hibernation) and are impacted by deforestation, however, the three tree-roosting species in Connecticut are especially vulnerable to loss or degradation of this habitat due to their reliance on tree cavities or other non-abundant tree habitats for both roosting and hibernation. The silver-haired bat, for example, requires old growth forest trees for habitat, however, a majority of the forest in Connecticut is new growth due to heavy harvesting of old growth forests in the past; this species is therefore rare and at risk of extirpation in Connecticut. 

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A species cannot recover when the habitat it depends on is disappearing, so any meaningful conservation efforts for Connecticut bats must involve the addressing of habitat loss and degradation concerns.