Active network solutions have been proposed to many of the problems caused by the increasing heterogeneity of the Internet. These ystems allow nodes within the network to process data passing through in several ways. Allowing code from various sources to run on routers introduces numerous security concerns that have been addressed by research into safe languages, restricted execution environments, and other related areas. But little attention has been paid to an even more critical question: the effect on end-to-end security of active flow manipulation. This thesis first examines the threat model implicit in active networks. It develops a framework of security protocols in use at various layers of the networking stack, and their utility to multimedia transport and flow processing, and asks if it is reasonable to give active routers access to the plaintext of these flows. After considering the various security problem introduced, such as vulnerability to attacks on intermediaries or coercion, it concludes not. We then ask if active network systems can be built that maintain end-to-end security without seriously degrading the functionality they provide. We describe the design and analysis of three such protocols: a distributed packet filtering system that can be used to adjust multimedia bandwidth requirements and defend against denial-of-service attacks; an efficient composition of link and transport-layer reliability mechanisms that increases the performance of TCP over lossy wireless links; and a distributed watermarking servicethat can efficiently deliver media flows marked with the identity of their recipients. In all three cases, similar functionality is provided to designs that do not maintain end-to-end security. Finally, we reconsider traditional end-to-end arguments in both networking and security, and show that they have continuing importance for Internet design. Our watermarking work adds the concept of splitting trust throughout a network to that model; we suggest further applications of this idea.