This volume chronicles the 16th Annual Conference on System Engineering Research (CSER) held on May 8-9, 2018 at the University of Virginia, Charlottesville, Virginia, USA. The CSER offers researchers in academia, industry, and government a common forum to present, discuss, and influence systems engineering research. It provides access to forward-looking research from across the globe, by renowned academicians as well as perspectives from senior industry and government representatives. Co-founded by the University of Southern California and Stevens Institute of Technology in 2003, CSER has become the preeminent event for researchers in systems engineering across the globe. Topics include though are not limited to the following: Systems in context: * Formative methods: requirements * Integration, deployment, assurance * Human Factors * Safety and Security Decisions/ Control & Design; Systems Modeling: * Optimization, Multiple Objectives, Synthesis * Risk and resiliency * Collaborative autonomy * Coordination and distributed decision-making Prediction: * Prescriptive modeling; state estimation * Stochastic approximation, stochastic optimization and control Integrative Data engineering: * Sensor Management * Design of Experiments