Recent developments in nanotechnology have enabled the manufacturing of low-power and low-cost nanoscale machines, i.e., nanomachines, with basic sensing, actuating and computing capabilities. Due to their size and simple structure, nanomachines individually have limited functionality. However, when they start to communicate to each other and construct nanonetworks, they are expected to collaboratively achieve more complex tasks and promise new solutions for several applications in biomedical, industry and military fields. Traditional computing and communications paradigms are not applicable due to the challenges posed by the physical laws governing this regime, and novel methods are required to realize nano networks. The main goals of the 3rd ACM International Conference on Nanoscale Computing and Communication (ACM NanoCom 2016), are to increase the visibilty of this growing research area to the wider computing and communication research communities as well as bring together researchers from diverse disciplines that can foster and develop new paradigms for nanoscale devices. Due to the highly inter-disciplinary nature of this field of research, the conference aims to attract researchers and academics from various areas of study such as electrical and electronic engineering, computer science, biology, chemistry, physics, mathematics, bioengineering, biotechnology, materials science, nanotechnology, who have an interest in computing and communications at the nanoscale.