Covert channels are means of communication that allow agents in a system to transfer information in a manner that violates the system’s security policy. Covert channels have been well studied in the constrained and old sense of the term where two agents are communicating through a channel while an intruder interferes to hide the transmission of a message. In an increasingly connected world where modern computer systems consist of broad and heterogeneous communication networks with many interacting agents, distributed covert channels are becoming increasingly available. For these distributed forms of covert channels, there are shortcomings in the science, mathematics, fundamental theory, and tools for risk assessment, and for proposing mechanisms and design solutions for averting these threats. Since current formal methods for specifying concurrent systems do not provide the tools needed to efficiently tackle the problem of distributed covert channels in systems of communicating agents, this thesis proposes Communicating Concurrent Kleene Algebra (C²KA) which is an extension to the algebraic model of concurrent Kleene algebra (CKA) first presented by Hoare et al. C²KA is used to capture and study the behaviour of agents, and description logic is used to capture and study the knowledge of agents. Using this representation of agents in systems of communicating agents, this thesis presents a formulation and verification approach for the necessary conditions for the existence of distributed covert channels in systems of communicating agents. In this way, this thesis establishes a mathematical framework for the modelling, analysis, and mitigation of distributed covert channels in systems of communicating agents. This framework enhances the understanding of covert channels and provides a basis for thinking and reasoning about covert channels in new ways. This can lead to a formal foundation upon which guidelines and mechanisms for designing and implementing systems of communicating agents that are resilient to covert channels can be devised. / Thesis / Doctor of Philosophy (PhD)