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An inversion method using a towed system consisting of a source and two receivers is presented. High-frequency chirp signals that have been emitted from the source are received after multiple penetrations and reflections from the shallow water sub-bottom structure and are processed for geoacoustical parameter estimation. The data are processed such that a good resolution and robustness is achieved via matched filtering, which requires information about the source signal. The inversion is formulated as an optimization problem, which maximizes the cost function defined as a normalized correlation between the measured and modeled signals directly in the time domain. The very fast simulated reannealing optimization method is applied to the global search problem. The modeled time signal is obtained using a ray approach. An experiment was carried out in the Mediterranean Sea using a towed source and receiver system. The inversion method is applied to the experimental data and results are found to be consistent with previous frequency-domain analyses using measurements from a towed horizontal array of receivers and measurements on a vertical array.