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A new generalized eigenstructure-based 3-dimensional joint estimator (GETJE) for the direction, frequency, and time-delay of multiple sources is presented. For 2-dimensional joint parameter estimation, we proposed an ESPRIT-based algorithm (Qunfei Zhang and Jianguo Huang, Int. Conf. On ASSP, 1999). Now we extend it to the 3-dimensional estimator. Using a single echo wave, the bearings, frequencies and time-delays of multiple reflectors are jointly estimated. We construct 2 sub-arrays like ESPRIT, and then conduct generalized eigen-decomposition for their auto-correlation matrix and cross-correlation matrix. Bearing parameters can be estimated from eigenvalues, while frequency parameters can also be obtained from corresponding eigenvectors. After modifying the time-delay vectors of the envelop of the emitting signal according to the estimated frequencies, the time-delay parameters can be obtained simultaneously. Computer simulations show that the GETJE can carry out the 3-dimensional joint parameter estimation without additional pairing in the case of lower SNR. Preferable results are also obtained in water tank experiments, which indicate that the GETJE is robust for sensor array errors and has potential applications.