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The Montreal Protocol has necessitated the changeover of chlorofluorocarbons (CFCs) to hydrofluorocarbons (HFCs) in Navy ships. Submarines represent a unique enclosed environment, and the use of HFCs has required adjustments in the operation of atmosphere control equipment. To ensure that the operational modifications would cause no significant changes in the composition of the submarine atmosphere, laboratory and shipboard studies were undertaken to model the effect of such modifications. Trace atmospheric constituents were measured with the shipboard Central Atmosphere Monitoring System (CAMS), a portable gas chromatograph, and retrospective sampling methodologies based on EPA methods for aldehydes, ketones and volatile organic compounds. The operation of atmosphere control equipment was adjusted and the composition of the submarine atmosphere was monitored in real-time and retrospectively.