Geomagnetic field signals have potential for use in underwater navigation and geophysical surveys. To map underwater geomagnetic fields, we propose a method that exploits an autonomous surface vehicle. In our system, a magnetometer is rigidly attached to the vehicle and not towed by a cable, minimizing the system’s size and complexity but requiring a dedicated calibration procedure due to magnetic distortion caused by the vehicle. Conventional 2D methods can be employed for the calibration by assuming the horizontal movement of the magnetometer, whereas the proposed 3D approach can correct for horizontal misalignment of the sensor. Our method does not require a supporting crane system to rotate the vehicle, and calibrates and maps simultaneously by exploiting data obtained from field operation. The proposed method has been verified experimentally in inland waters, generating a magnetic field map of the test area that is of much higher resolution than the public magnetic field data.