For synthetic aperture imaging, position and orientation deviation is of great concern. Unknown motions of a Synthetic Aperture Sonar (SAS) can blur the reconstructed images and degrade image quality considerably. Considering the high sensitivity of synthetic aperture imaging technique to sonar deviation, this research aims at providing a thorough navigation solution for a free-towed synthetic aperture sonar (SAS) comprising aspects from the design and construction of the navigation card through to data postprocessing to produce position, velocity, and attitude information of the sonar. The sensor configuration of the designed navigation card is low-cost Micro-Electro-Mechanical-Systems (MEMS) Magnetic, Angular Rate, and Gravity (MARG) sensors including three angular rate gyroscopes, three dual-axial accelerometers, and a triaxial magnetic hybrid. These MARG sensors are mounted orthogonally on a standard 180mm Eurocard PCB to monitor the motions of the sonar in six degrees of freedom. Sensor calibration algorithms are presented for each individual sensor according to its characteristics to precisely determine sensor parameters. The nonlinear least square method and two-step estimator are particularly used for the calibration of accelerometers and magnetometers. A quaternion-based extended Kalman filter is developed based on a total state space model to fuse the calibrated navigation data. In the model, the frame transformations are described using quaternions instead of other attitude representations. The simulations and experimental results are demonstrated in this thesis to verify the capability of the sensor fusion strategy.