Many tropical landscapes are changing rapidly, with uncertain outcomes for biodiversity, landscape function, and the corresponding landscape services. Therefore, monitoring and adaptively managing the drivers and consequences of landscape change while sustaining the production of essential resources have become research and policy priorities. In this perspective, we have applied a recent framework, the stochastic dynamic methodology (StDM), with the purpose of understanding the effects of natural and anthropogenic disturbances on caves' integrity using cave beetle communities (Coleoptera) as ecological indicators. The proposed method was preceeded by a generalized linear model for discriminating significant relationships between the selected indicators, the structural changes in the caves, and the epigean habitats associated. The obtained results showed different ecological trends in response to the environmental changes. Overall, the simulation results seem to demonstrate the StDM reliability in determining the effects of habitat dynamics, that is, the expansion of agricultural activities, in areas near the caves in the structure of cave beetle communities. The applied method, based on universal information-theoretic principles, can be easily implemented and interpreted by environmental managers and decision makers, enabling anticipating impacts and supporting the development of measures aimed at minimizing the identified problems.