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Hermes is an underwater acoustic modem that achieves very high-bit rate digital communications in ports and shallow waters. In its current form, this modem supports only Single-Input Single-Output communications. In this paper, the authors investigate the use of Multiple-Input-Multiple-Output (MIMO) technology. MIMO, applied to underwater acoustic (UWA) communications, has shown great promise in terms of improvements of data rate, flexibility and coverage area. The MIMO system developed here combines Hadamard training sequences and the traditional Hermes uplink message. Key to proper MIMO communications is an accurate channel least-square estimation and equalization. A MIMO equalization process consisting of a matrix-based linear filter optimized under the minimum mean square error (MMSE) criterion is presented here. The channel estimation technique is evaluated using simulated messages generated by a very shallow water Rician channel model. Simulation results indicate that a fading channel can be estimated with an RMSE of 0.191% on average at 75m under realistic conditions. In the sole presence of specular reflections, the mean value of the root mean square error (RMSE) is 94.59% before equalization and 32.26% after equalization. The variance of the RMSE is 32.014% before equalization and 12.77% after equalization, respectively. In the presence of sound scattering and using every echo, the mean value of the RMSE is 54.27% after equalization, vs. 120.55% before equalization.