The number of researchers and institutions moving to the utilization of zebrafish for biomedical research continues to increase because of the recognized advantages of this model. Numerous factors should be considered before building a new or retooling an existing facility. Design decisions will directly impact the management and maintenance costs. We and others have advocated for more rigorous approaches to zebrafish health management to support and protect an increasingly diverse portfolio of important research. The Sinnhuber Aquatic Research Laboratory (SARL) is located ∼3 miles from the main Oregon State University campus in Corvallis, Oregon. This facility supports several research programs that depend heavily on the use of adult, larval, and embryonic zebrafish. The new zebrafish facility of the SARL began operation in 2007 with a commitment to build and manage an efficient facility that diligently protects human and fish health. An important goal was to ensure that the facility was free of Pseudoloma neurophilia (Microsporidia), which is very common in zebrafish research facilities. We recognize that there are certain limitations in space, resources, and financial support that are institution dependent, but in this article, we describe the steps taken to build and manage an efficient specific pathogen-free facility.