Mobile dental delivery systems (MDDSs) are receiving growing interest for reaching isolated patients, as well as in dental care for fragile and hospitalized patients, with the advantage of being able to be used from room to room or during general anesthesia (GA) in an operating room. Therefore, ensuring the care safety is crucial. The aim of this study was to elaborate and assess an MDDS maintenance protocol, containing the management of dental unit waterlines and adapted to specific conditions such as dental care under GA. A step-by-step protocol was established and implemented for an MDDS used during dental care under GA in children. Samples of the output water were collected at J0, J+1, 3, 6, 12, and 24 months, and cultured to observe the microbiological quality of the water. All the results (heterotrophic plate count at 22 °C, at 37 °C, and specific pathogenic germs sought) showed an absence of contamination. The protocol presented was effective over time and allowed ensuring the safety of care to be ensured when using MDDS, even during dental procedures under GA. As a result, it could be implemented by any dental care delivery structure wanting to reinforce the safety of its practice.