The paper analyses differences between dome and flat port housings used for underwater photogrammetry. The underwater environment negatively affects image quality and 3D reconstructions, but this influence on photogrammetric measurements, so far, has not been addressed properly in the literature. In this work, motivations behind the need for systematic underwater calibrations are provided, then experimental tests using a specifically designed photogrammetric modular test object in laboratory and at sea are reported. The experiments are carried out using a Nikon D750 24 Mpx DSLR camera with a 24 mm f2.8 AF/D lens coupled with a NIMAR NI3D750ZM housing, equipped first with a dome and, successively, with a flat port. To quantify the degradation of image quality, MTF measurements are carried out, then the outcomes of self-calibrating bundle adjustment calibrations are shown and commented. Optical phenomena like field curvature as well as chromatic aberration and astigmatism are analysed and their implications on the degradation of image quality is factored in the bundle adjustment through a different weighting of 2D image observations.