Climate change is fundamentally reshaping the landscape of infectious diseases by altering pathogen evolution, transmission dynamics, and host–vector interactions. Rising temperatures, extreme climatic events, and environmental disruption are expanding the geographic range of many pathogens, driving outbreaks in previously unaffected regions and revealing major limitations in existing surveillance systems. Integrated, genomics-driven surveillance frameworks provide a powerful approach to improve the detection, characterization, and anticipation of emerging and reemerging viral threats. Climate-linked factors—including increasing temperatures, flooding, droughts, and human displacement—are accelerating the spread of mosquito-borne and waterborne pathogens, creating conditions conducive to more frequent and severe epidemics. Applications of genomic epidemiology during major outbreak events, such as the emergence of Zika virus in Brazil, illustrate how high-resolution sequencing data can be leveraged to reconstruct transmission dynamics in real time. Recent advances in sequencing technologies, including amplicon-based long-read strategies, have further enabled rapid and scalable genomic surveillance of RNA viruses, particularly arboviruses. Beyond sequencing alone, the integration of genomic, epidemiological, ecological, mobility, and climate data supports phylodynamic and spatial modelling approaches capable of quantifying viral dispersal, identifying key drivers of transmission, and predicting areas at future risk under evolving climate scenarios. The application of these integrated systems in diverse real-world settings, including Europe and Africa, demonstrates how recent introductions and lineage expansions of dengue and chikungunya viruses reflect the combined effects of climate-driven range expansion and surveillance gaps. Collectively, these findings underscore the critical role of multidisciplinary, genomics-informed surveillance systems in strengthening global preparedness and guiding timely public health responses in the context of accelerating environmental change.