In recent years, the Oceanographic and Hydrographic Research Center (part of the General Maritime Directorate of Colombia (DIMAR) has made important efforts to advance research in the field of marine geophysics, in particular, the techniques of geomagnetism, sub-bottom profiling, and side-scan sonar, the first being the most developed at the present time. A method is presented for the acquisition of geomagnetic data in marine environments, as used by DIMAR in the Colombian maritime territory. The development of the geomagnetic method not only offers the opportunity to advance basic scientific knowledge, but it is also of great importance in support of national sovereignty issues. Among other applications, the most representative uses of the geomagnetic method are the location of pipelines and metal plates, detection of buried ordnance, identification of sites of archaeological interest, and the identification and characterization of geological structures. As a result of testing the method, a grid of geomagnetic data was surveyed in an area close to the Island of San Andrés in the north-west of the Colombian maritime territory. The survey was prepared with a regional geometric arrangement, the result of which was compared with survey data obtained from the National Oceanic and Atmospheric Administration (NOAA) magnetic data repository and carried out in the same study area. Despite the long time interval between the two surveys, almost 50 years, no significant differences were observed in terms of the analyzed variables. Finally, results show negligible differences between the magnetic data obtained for the years 1970 and 2018 for all the variables measured, such as the inclination, declination, and total magnetic field. These differences may be attributable to a geological component or also to the acquisition and processing methods used in the 1970s.