In detecting threats, particularly explosives, the challenge is to design a system with acceptable detection probability and false-alarm rate that does not unduly inconvenience travelers. Ferry passengers, in particular, are less likely than aviation passengers to tolerate extra delays for extensive scrutiny of themselves or their personal belongings. Similarly, substantial purchase and deployment costs of equipment by ferry owners and operators would not be tenable for small improvements in security. Thus, this paper analyzes different approaches to security and how best to combine detection capabilities and people to enhance ferry transportation security without affecting mobility. Several factors must be considered in choosing practical combinations of detectors to provide the best possible security system. Those factors and their interrelationships are examined within the context of different architectures. Besides the throughput analysis, the manuscript presents a general framework to compare security system designs and implement efficient and effective alternatives for ferry transportation.