A marine INS/GPS (inertial navigation system/global positioning system) adaptive navigation system is presented in this paper. The GPS with two antennae providing vessel attitude is selected as the auxiliary system to fuse with INS. The Kalman filter is the most frequently used algorithm in the integrated navigation system, which is capable of estimating INS errors online based on the measured errors between INS and GPS. The conventional Kalman filter (CKF) assumes that the statistics of the noise of each sensor are given. As long as the noise distributions do not change, the Kalman filter will give the optimal estimation. However, the GPS receiver will be disturbed easily and thus temporally changing measurement noise will join into the outputs of GPS, which will lead to performance degradation of the Kalman filter. Many researchers introduce a fuzzy logic control method into innovation-based adaptive estimation Kalman filtering (IAE-AKF) algorithm, and accordingly propose various adaptive Kalman filters. However, how to design the fuzzy logic controller is a very complicated problem, which is still without a convincing solution. A novel IAE-AKF is proposed herein, which is based on the maximum likelihood criterion for the proper computation of the filter innovation covariance and hence of the filter gain. The approach is direct and simple without having to establish fuzzy inference rules. After having deduced the proposed IAE-AKF algorithm theoretically in detail, the approach is tested in the developed INS/GPS integrated marine navigation system. Real field test results show that the adaptive Kalman filter outperforms the CKF with higher accuracy and robustness. It is demonstrated that this proposed approach is a valid solution for the unknown changing measurement noise existing in the Kalman filter.