Underwater mass spectrometry systems can be used for direct in situ detection of volatile organic compounds and dissolved gases in oceans, lakes, rivers and waste-water streams. In this work we describe the design and operation of (1) a linear quadrupole mass filter and (2) a quadrupole ion trap mass spectrometer interfaced, in each case, with a membrane introduction/fluid control system and packaged for underwater operation. These mass spectrometry systems can operate autonomously, or under user control via a wireless rf link. Detection limits for each system were determined in the laboratory using pure solutions. The quadrupole mass filter system provides detection limits in the 1-5 ppb range with an upper mass limit of 100 amu. Its power requirement is approximately 95 Watts. The ion trap system has detection limits well below 1 ppb, an upper mass limit of 650 amu and MS/MS capability. Its power consumption is on the order of 150 Watts. The present membrane limits analysis to non-polar compounds (<300 amu) with analysis cycles of 5-15 minutes. Deployments of both types of instruments are described, along with a discussion of the challenges associated with in-water mass spectrometry and descriptions of alternative in-water mass spectrometer configurations.