Rapid reaction screening in flow systems may help to reduce the time and material required to optimize, scale-up, and implement a flow process. Compartmentalization using small fluorous plugs has been implemented in several commercial reactors as a means for running a large number of isolated reactions in series within a flow reactor. Dye tracking, visual mixing, and reactivity studies are used to better understand the factors controlling dispersion within a commercial reactor. The role of dispersion on reactivity is elucidated using model reactions, and an optimized method for performing high-throughput screening is proposed.