Ecological thresholds represent a critical tipping point along an environmental gradient that, once breached, can have irreversible consequences for species persistence and assemblage structure. Thresholds can also be used to identify species with the greatest sensitivity to environmental changes. Bats are keystone species yet are under pressure from human disturbances, specifically landscape and cave disturbances (i.e., reduced forest cover, urbanization, hunting, tourism). We compared bat assemblages across environmental and disturbance gradients measured at 56 caves in the Philippines to identify species-specific thresholds and assess congruence among species responses. All species exhibited significant responses to one or more gradients, with 84% responding to more than one gradient. Yet mixed responses of sensitivity to some gradients but tolerance to others hindered identification of assemblage thresholds to all gradients except landscape disturbance. However, we identified credible indicator species that exhibit distinct thresholds to specific gradients and tested for differences in ecological and morphological traits between species groups with shared responses (i.e., negative or positive). Few traits were useful for discriminating the direction of a species response, with some exceptions. Species that responded positively to increased landscape disturbance and hunting had greater body mass, whereas species that responded negatively to mining emitted higher peak call frequencies.