Climate change has significantly altered the distribution, abundance, and activity of environmental microbes (e.g., bacteria, viruses, fungi), thereby modifying the transmission dynamics of microbe-driven diseases. This study integrates environmental microbiology, epidemiology, and AI-based modeling to explore how rising temperatures, extreme precipitation, and sea-level rise affect microbe survival, proliferation, and dissemination in air, water, and soil. We analyzed epidemiological data from 12 countries to quantify the association between climate variables, microbial contamination, and disease outbreaks (e.g., cholera, dengue, aspergillosis). Innovative analytical methods (e.g., metagenomic sequencing, qPCR) were used to characterize microbial communities in environmental matrices, while bioinformatics tools identified key pathogenic strains and their antibiotic resistance genes. Additionally, we evaluated the effectiveness of adaptive strategies (e.g., improved water sanitation, early warning systems) in mitigating disease risks. The results highlight the urgent need for integrated climate and public health policies to address microbe-driven disease threats in a changing environment.