Comprehensive investigations of geophysical fields (GPF) of the ocean are among the top priority problems in underwater robotics. Problems reside in developing automated systems capable of real-time operation for gathering, accumulating, and processing diverse geophysical information. The data’s total volume is applied for long-term or real-time monitoring of marine areas, environment or objects surveillance, mapping certain regions, or anomalies in geographical coordinates. One of the main elements of such systems is the computational models sensitive to properties of geophysical fields, features of search routes of underwater vehicles, and particular aspects of missions performed during trajectory measurements and features of navigational support tasks. The work considers computational models of comprehensive interpretation of the results of trajectory measurements of geophysical fields using an autonomous underwater vehicle (AUV), and estimation of accuracy of map-aided navigation on the reconstructed map of geophysical fields. Algorithms and software consider distinctive features of representation of bathymetry, magnetometry, and gravimetry data visualized in 2D and 3D. Algorithm of map-aided navigation by the reconstructed fields is discussed. The final assessments of the considered models’ accuracy consider averaged errors of measurements, mapping, and inertial navigation. Obtained assessments are based on theoretical investigations, results of model experiments, and experimental trials of AUV’s systems under actual operating conditions.