Few instruments exist that can image microscopic marine organisms in their natural environment so that their locomotion mechanisms, feeding habits, and interactions with surfaces, such as biofouling, can be investigated in situ. We describe here the design and performance of a simple submersible digital in-line holographic microscope that can image organisms and their motion with micron resolution and that can be deployed from small vessels. Holograms and reconstructed images of several microscopic aquatic organisms were successfully obtained down to a depth of 20m. Important microscope characteristics such as the effect of camera pixel size on lateral and depth resolutions as well as the maximum sample volume that can be imaged with a given resolution are discussed in detail.