The strapdown inertial navigation system (SINS) with integrated Doppler velocity log (DVL) is widely utilised in underwater navigation. In the complex underwater environment, however, the DVL information may be corrupted, and as a result the accuracy of the Kalman filter in the SINS/DVL integrated system degrades. To solve this, an adaptive Kalman filter (AKF) with measurement noise estimator to provide noise statistical characteristics is generally applied. However, existing methods like moving windows (MW) and exponential weighted moving average (EWMA) cannot adapt to a dynamic environment, which results in unsatisfactory noise estimation performance. Moreover, the forgetting factor has to be determined empirically. Therefore, this paper proposes an improved EWMA (IEWMA) method with adaptive forgetting factor for measurement noise estimation. First, the model for a SINS/DVL integrated system is established, then the MW and EWMA based measurement noise estimators are illustrated. Subsequently, the proposed IEWMA method which is adaptive to the various environments without experience is introduced. Finally, simulation and vehicle tests are conducted to evaluate the effectiveness of the proposed method. Results show that the proposed method outperforms the MW and EWMA methods in terms of measurement noise estimation and navigation accuracy.