The measurement of porosity and permeability in shallow-water carbonates is often complicated by the nature and degree of diagenesis, as well as the issue of scale-dependence in the measurement technique. Vertical profiles of hydraulic conductivity were calculated from short-interval straddle-packer injection tests in a three-well transect across the Pleistocene reefal limestone of the southern Dominican Republic (DR). Combined with whole-core porosity estimates and small-diameter (2.54 cm) plug estimates of matrix porosity and permeability, these data provide a means of assessing the scale-dependent petrophysical variability within a complex carbonate pore system, as well as the primary factors that control flow within such a system. Interval permeability values (converted from hydraulic conductivity) based on in situ injection tests ranged between 5 and 25 Darcy (D) (12.2 D geometric mean), up to three orders of magnitude higher than associated plug permeability values (0.08 D geometric mean). Although plug permeability is related to depositional environment (backreef, reef crest, forereef), injection tests did not show a relation to environment. Furthermore, interval permeabilities showed no relation to “matrix” (plug-based) porosity or permeability values. Interval injection permeability was correlated to “total” (whole-core) porosity and, even more so to larger scale “vuggy” (>~5 mm) porosity, quantified by subtracting the plug-based “matrix” porosity from the whole-core “total” porosity. The differences in permeability between plug and interval injection tests for these vuggy carbonates becomes greater over time, since cementation occludes matrix porosity and dissolution opens up larger molds and vugs, especially corals and other large aragonitic grains. The in situ interval permeability values measured in the DR reefal carbonates provide better values (than plug or core) of the impact of early meteoric diagenesis. These results confirm early development of vuggy intervals that can have permeability that is orders of magnitude greater than measured plug permeabilities. A touching-vug pore system shifts the scale dependence of hydraulic conductivity from the plug scale to the packer (bed) scale and probably toward the regional scale.