Laboratory data and computer tomography (CT) scan image analysis of carbonate rocks were combined demonstrating a quantitative link between acoustic and transport properties, the fraction of microcrystalline calcite (micrite) in the matrix, and the grain-to-micrite matrix ratio. Samples from the Monte Acuto formation, Gargano, Italy, a transgressive system tract (TST) whose microstructure ranges from basal pelagic mudstones to coarse calciturbidites, were analyzed. Results indicate that high micrite rocks with low grain-to-micrite matrix ratios, typical of low-energy depositional settings, are relatively stiffer and more impermeable. In contrast, lower amounts of micrite, due to high-energy depositional settings or its removal from intergranular macropores by progressive leaching of the matrix, leads to high grain-to-micrite matrix ratios. This process will increase porosity and reduce rock stiffness, both of which reduce velocity. Decreasing micrite content correlates well with increasing macroporosity. Permeability increases with macroporosity, as microporosity within micrite does contribute less significantly to fluid flow. Study results, the mechanisms producing porosity, and the classifications describing carbonate rocks in the literature prompted us to address the characterization of these rocks from a different perspective: linking the transport and acoustic properties directly to the content of the microcrystalline matrix rather than to the type and/or geometry of the pore space left behind. These trends of the acoustic and transport properties particularly apply to cycles deposited in transgressive system tracts.