Cameras can be considered measurement devices complementary to acoustic sensors when it comes to surveying marine environments. When calibrated and used correctly, these visual sensors are well-suited for automated detection, quantification, mapping, and monitoring applications and when aiming at high-accuracy 3D models or change detection. In underwater scenarios, cameras are often set up in pressure housings with a flat glass window, a flat port, which allows them to observe the environment. In this contribution, a geometric model for image formation is discussed that explicitly considers refraction at the interface under realistic assumptions like a slightly misaligned camera (w.r.t. the glass normal) and thick glass ports as common for deep sea applications. Then, starting from camera calibration, a complete, fully automated 3D reconstruction system is discussed that takes an image sequence and produces a 3D model. Newly derived refractive estimators for sparse two-view geometry, pose estimation, bundle adjustment, and dense depth estimation are discussed and evaluated in detail.