Underwater is a complex structured environment because of inhomogeneous light absorption and light scattering by the environment. These factors make 3D reconstruction in underwater more challenging. In the literature, only calibrated cameras and predefined camera motions are allowed for 3D reconstruction. In this study, 3D representation of underwater scenes are reconstructed from uncalibrated video sequences.3D reconstruction consists Of the following stages: Image enhancement, feature defection and matching, fundamental matrix estimation, auto-calibration, recovery of extrinsic parameters, rectification, stereo matching and dense reconstruction. In this paper, various algorithms are implemented for each stage and the best performing ones for underwater applications are defined. As a result, a single camera based automatic 3D modelling system, which is reads, to be used in underwater applications, is developed.