The problem of secure underwater communication can take advantage of the exploitation of quantum resources and novel quantum technologies. At variance with the current experiments performed at the single photon level, here we propose a different scenario involving mesoscopic twin-beam states of light and two classes of commercial photon-number-resolving detectors. We prove that twin-beam states remain nonclassical even if the signal propagates in tubes filled with water, while the idler is transmitted in free space. We also demonstrate that from the study of the nonclassicality information about the loss and noise sources affecting the transmission channels can be successfully extracted.