In this study, we introduce a new calibration method for underwater optical stereo scanners. It uses air calibration, additional underwater parameters, and extended camera modeling. The new methodology can be applied to both passive photogrammetric and structured light three-dimensional (3D) scanning systems. The novel camera model uses a variable principal distance depending on the radial distance to the principal point instead of two-dimensional distortion functions. This allows for an initial improvement of 3D reconstruction quality. In a second step, certain underwater-specific parameters—such as refraction indices, glass thickness, and view-port distances—are determined. Finally, a correction function for the entire measurement volume can be obtained from a few underwater measurements. Its application further improves the measurement accuracy. Measurement examples show the performance of the new calibration method in comparison to current underwater calibration strategies. A discussion of the possibilities and limits of the new calibration method and an outlook for future work complete this work.