Abstract The Florida Keys offer an outstanding setting to study the diagenetic environment of one interglacial (the present) superimposed on limestones that formed during earlier interglacials. It has been shown by others that the surficial Miami Formation (oolitic facies) and Key Largo Formation (reef facies) of Big Pine Key were deposited during the last interglacial (unit Q5 of the local time stratigraphy; Q = Quaternary) and are underlain by Key Largo Formation of earlier interglacials (units Q4 and Q3). Mapping of the freshwater/saltwater interface beneath the lenses at Big Pine Key shows that the lenses are considerably foreshortened near the base of the Q5 unit. Dupuit-Ghyben-Herzberg (DGH) modeling of the northern lens indicates an order-of-magnitude contrast in hydraulic conductivity between the Q5 and pre-Q5 limestones, in addition to an order-of-magnitude contrast in hydraulic conductivity between the Q5 and modern analogs. Differences of such magnitude attest to the significance of secondary permeability in these Pleistocene limestones. DGH flow-net analysis shows that the distribution of freshwater discharge, pore-volume flushing rate, and residence time along flowlines are all significantly affected by the presence of the buried, higher permeability limestones. The case study, therefore, illustrates how the development of secondary porosity and permeability during early meteoric diagenesis feeds back as a stratigraphic control on groundwater flow during continued meteoric exposure.