San Juan County maintains a 72-hour holding facility in Friday Harbor. Commitments from the court system that exceed 48 hours are transferred to Island County Correctional Facility in Coupeville. Visiting inmates in Friday Harbor is limited to family members only, and only as staffing permits. All persons taken into custody on islands other San Juan are transferred to the Friday Harbor holding facility.

The Sheriff's Office operates an electronically home monitored work program for selected inmates. Inmates on this program work on projects that are designed to benefit the county tax-payer. Some inmates participate in a Work Release program where they are permitted to maintain regular employment but are restricted to their home except when at work. These work programs operate 7 days a week and are supervised by Dan Seaton and Andy Urbach.