The TETHYS mass spectrometer is intended for long-term in situ observation of dissolved gases and volatile organic compounds in aquatic environments. Its design maintains excellent low mass range sensitivity and stability during long-term operations, enabling characterization of low-frequency variability in many trace dissolved gases. Results are presented from laboratory trials and a 300-h in situ trial in a shallow marine embayment in Massachusetts, U.S.A. This time series consists of over 15000 sample measurements and represents the longest continuous record made by an in situ mass spectrometer in an aquatic environment. These measurements possess sufficient sampling density and duration to apply frequency analysis techniques for study of temporal variability in dissolved gases. Results reveal correlations with specific environmental periodicities. Numerical methods are presented for converting mass spectrometer ion peak ratios to absolute-scale dissolved gas concentrations across wide temperature regimes irrespective of ambient pressure, during vertical water column profiles in a hypoxic deep marine basin off the coast of California, U.S.A. Dissolved oxygen concentration values obtained with the TETHYS instrument indicate close correlation with polarographic oxygen sensor data across the entire depth range. These methods and technology enable observation of aquatic environmental chemical distributions and dynamics at appropriate scales of resolution.