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We investigate the deployment of a submersible platform with stereovision imaging capability for three-dimensional (3D) mapping of benthic habitats and other sea-floor structures over local areas. A complete framework is studied, comprising: 1) suitable trajectories to be executed for data collection; 2) data processing for positioning and trajectory followed by online frame-to-frame and frame-to-mosaic registration of images, as well as recursive global realignment of positions along the path; and 3) 3D mapping by the fusion of various visual cues, including motion and stereo within a Kalman filter. The computational requirements of the system are evaluated, formalizing how processing may be achieved in real time. The proposed scenario is simulated for testing with known ground truth to assess the system performance, to quantify various errors, and to identify how performance may be improved. Experiments with underwater images are also presented to verify the performance of various components and the overall scheme.