This dataset comprises morphometric data of pores and pore throats extracted from micro-CT images of carbonate plugs from the Barra Velha Formation (Santos Basin – Brazilian Pre-Salt). High-resolution 3D images were segmented to identify pores and throats, and to quantify their geometric characteristics such as radius, volume and coordination number. These data support the investigation of pore-scale heterogeneities and the connectivity of complex pore systems in lacustrine carbonate reservoirs.