Background: Event-based social media monitoring and pathogen whole genome sequencing (WGS) will enhance communicable disease surveillance research and systems. If linked electronically and scanned systematically, the information provided by these technologies could be mined to uncover new epidemiological patterns and associations much faster than traditional public health approaches. The benefits of earlier outbreak detection are significant, but implementation could be opposed in the absence of a social licence or if ethical and legal concerns are not addressed. Methods: A three-phase mixed-method Delphi survey with Australian policy-makers, health practitioners and lawyers (n = 44) was conducted to explore areas of consensus and disagreement over (1) key policy and practical issues raised by the introduction of novel communicable disease surveillance programmes; and (2) the most significant and likely risks from using social media content and WGS technologies in epidemiological research and outbreak investigations. Results: Panellists agreed that the integration of social media monitoring and WGS technologies into communicable disease surveillance systems raised significant issues, including impacts on personal privacy, medicolegal risks and the potential for unintended consequences. Notably, their concerns focused on how these technologies should be used, rather than how the data was collected. Panellists held that social media users should expect their posts to be monitored in the interests of public health, but using those platforms to contact identified individuals was controversial. The conditions of appropriate use of pathogen WGS in epidemiological research and investigations was also contentious. Key differences amongst participants included the necessity for consent before testing and data-linkage, thresholds for action, and the legal and ethical importance of harms to individuals and commercial entities. The erosion of public trust was seen as the most significant risk from the systematic use of these technologies. Conclusions: Enhancing communicable disease surveillance with social-media monitoring and pathogen WGS may cause controversy. The challenge is to determine and then codify how these technologies should be used such that the balance between individual risk and community benefit is widely accepted. Participants agreed that clear guidelines for appropriate use that address legal and ethical concerns need to be developed in consultation with relevant experts and the broader Australian public.