This paper addresses the lack of “push-button” software for optical marine imaging, which currently limits the use of photogrammetric approaches by a wider community. It presents and reviews an open source software, Matisse, for creating textured 3D models of complex underwater scenes from video or still images. This software, developed for non-experts, enables routine and efficient processing of underwater images into 3D models that facilitate the exploitation and analysis of underwater imagery. When vehicle navigation data are available, Matisse allows for seamless integration of such data to produce 3D reconstructions that are georeferenced and properly scaled. The software includes pre-processing tools to extract images from videos and to make corrections for color and uneven lighting. Four datasets of different 3D scenes are provided for demonstration. They include both input images and navigation and associated 3D models generated with Matisse. The datasets, captured under different survey geometries, lead to 3D models of different sizes and demonstrate the capabilities of the software. The software suite also includes a 3D scene analysis tool, 3DMetrics, which can be used to visualize 3D scenes, incorporate elevation terrain models (e.g., from high-resolution bathymetry data) and manage, extract, and export quantitative measurements for the 3D data analysis. Both software packages are publicly available.