Pilot plant systems are generally designed to reflect conditions of a particular full-scale system for the purpose of studying the impact of drinking water treatment changes, effectiveness for the removal of contaminants and the addition of new unit processes and practices. Pilot testing potential mitigation strategies is a recommended procedure to research optimal water quality treatment variables and avoid implementing a strategy that may not work for unforeseen reasons. This document is a comprehensive design manual that summarizes the activities and experiences of an EPA research team which was assembled to address Cryptosporidium contamination of drinking water, as well as other research needs. All of the team members had significant experience with filtration studies or in designing, fabricating, or operating pilot plant systems. The team concluded that the best, most meaningful way to conduct the needed research was to design, build, and operate a ‘mini pilot plant.’ The team designed and constructed a prototype 450 milliliter per minute conventional flocculation, sedimentation, and filtration facility. Final design specifications of individual processes were summarized and compared to other pilot- and full-scale systems. While originally designed for Cryptosporidium research, the system was built to allow relatively simple, fast, and inexpensive modifications for other studies.