This research presents a network-based simulation approach to model the impacts of species extinction and habitat loss on ecological networks, with a particular focus on the Amazon ecosystem. By constructing weighted directed networks that represent species interactions, we identify keystone species through centrality measures and assess their critical roles in maintaining ecosystem stability. Using community detection algorithms, we uncover the modular structure of these interactions, revealing key patterns of interdependence within the network. Novel simulations of environmental disturbances—such as habitat fragmentation, patch loss, and species migration—further explore how these disruptions affect network structure, biodiversity, and overall ecosystem resilience. The findings offer valuable insights into ecosystem vulnerability and provide actionable guidance for conservation strategies aimed at mitigating biodiversity loss in fragile ecosystems.