This article considers tracking a constant-velocity underwater target, which emits sound with distinct frequency lines. By analyzing the target’s azimuth, elevation and multiple frequency lines, the ownship can estimate the target’s position and (constant) velocity. In our paper, this tracking problem is called the 3D Angle-Frequency Target Motion Analysis (AFTMA) problem. We consider the case where some frequency lines disappear and appear occasionally. Instead of tracking every frequency line, this paper proposes to estimate the average emitting frequency by setting the average frequency as the state vector in the filter. As the frequency measurements are averaged, the measurement noise decreases. In the case where we use the average frequency line as our filter state, both the computational load and the root mean square error (RMSE) decrease, compared to the case where we track every frequency line one by one. As far as we know, our manuscript is unique in addressing 3D AFTMA problems, such that an ownship can track an underwater target while measuring the target’s sound with multiple frequency lines. The performance of the proposed 3D AFTMA filter is demonstrated utilizing MATLAB simulations.