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Considering the influence of measurement error on target state estimation, there is an uncertain dispersion region for target position estimate, that is, the area of uncertainty (AOU, area of uncertainty). In underwater target tracking, the state estimation is point estimation without AOU estimation and its accuracy is poor in the early stage because of large measurement errors. Fast tracking with higher accuracy and AOU estimation are of great significance to time-sensitive target tracking. To improve the state estimation accuracy in the early stage, and estimate the AOU, a method of AOU estimation of underwater moving target is presented based on a stochastic maneuvering motion (SMM, stochastic maneuvering motion) model. The stochastic maneuvering motion model is established based on the Langevin equation to reflect the movement characteristics of an underwater moving target. Then, the target state is estimated with a noise adaptive Kalman filter by constructing the measurement equation and state equation according to measurement error characteristic and stochastic maneuvering model. Based on the physical significance of the error covariance matrix from the Kalman filter, the parameters of AOU are deduced. Simulation results of underwater target tracking and AOU estimation are presented to demonstrate the relative performance of the proposed algorithm compared with the adaptive Kalman filter. It is clearly shown from the results that SMM tracking algorithm achieves higher accuracy of state estimation in the initial stage of tracking, and the predicted AOU is consistent with the actual distribution of underwater moving targets while yielding more concentrated distribution, which reveals that estimated AOU can be precisely represented by the confidence ellipses. The presented approach and obtained results may be useful in time-sensitive target threat analysis and weapon strike applications.