Emerging infectious diseases affecting humans and wildlife have increasingly come into the public awareness and been identified as critical concerns for species conservation. The COVID- 19 pandemic has tragically realized the threat of novel pathogens spilling over into new hosts and new environments. Many inadequacies of pathogen monitoring and modeling have also been laid bare, including the complications surrounding pathogens infecting multiple host species. My dissertation work examines the application and comparative effectiveness of different modeling tools to two prominent EIDs: White-nose syndrome (WNS) in North American bats and SARS- CoV-2 spillover from human households to free-ranging and feral cats. In the first chapter of this dissertation, I examined the landscape characteristics of known hibernacula, which function as reservoirs for a fungal pathogen, for three bat species affected by WNS: little brown bat (Myotis lucifugus), big brown bat (Eptesicus fuscus), and the Indiana bat (Myotis sodalis). Geological and hydrological variables provided the greatest portion of predictive power for landscape suitability of M. lucifugus and M. sodalis hibernacula. The suitability model for E. fuscus, known for more diffuse and generalist occupancy of roosts, was mostly driven by climatic and topographic variables. The genetic relatedness of a known collection of M. lucifugus hibernacula were compared to the intervening landscape suitability measures between hibernacula. The second and third chapters applied multi-population infectious disease models layered on spatial colony maps. For the second chapter, WNS spread was simulated for M. lucifugus and E. fuscus hibernacula to test the properties of multi-species disease models. The combination of two species, despite M. lucifugus far outnumbering E. fuscus, reduced predictive divergence from observed timings of WNS arrival. The third chapter applies these multi-population disease spread principles to spillover modeling of SARS-CoV-2 in domestic and feral cats. This model concludes that indoor-outdoor cats and feral cats can form a short-term reservoir of SARS-CoV-2 for up to two years, but cats are unlikely to be a persistent long-term reservoir. The model here is the first to assess the risk of SARS-CoV-2 natural reservoir formation in cats and evaluates effects of population densities and interaction rates.