GPS and low-cost INS sensors are widely used for positioning and attitude determination applications. Low-cost inertial sensors exhibit large errors that can be compensated using position and velocity updates from GPS. Combining both sensors using a Kalman filter provides high-accuracy, real-time navigation. A conventional Kalman filter relies on the correct definition of the measurement and process noise matrices, which are generally defined a priori and remain fixed throughout the processing run. Adaptive Kalman filtering techniques use the residual sequences to adapt the stochastic properties of the filter on line to correspond to the temporal dependence of the errors involved. This paper examines the use of three adaptive filtering techniques. These are artificially scaling the predicted Kalman filter covariance, the Adaptive Kalman Filter and Multiple Model Adaptive Estimation. The algorithms are tested with the GPS and inertial data simulation software. A trajectory taken from a real marine trial is used to test the dynamic alignment of the inertial sensor errors. Results show that on line estimation of the stochastic properties of the inertial system can significantly improve the speed of the dynamic alignment and potentially improve the overall navigation accuracy and integrity.