Oil and gas reside in reservoirs within peritidal and shallow subtidal lagoonal carbonate sediments across the globe. This is a zone of facies heterogeneity, controlled by changes in depositional energy, water depth, clastic influx, and evapotranspiration. Close proximity to evaporitic brine pools means that it is also an environment with the potential for dolomitization during shallow burial. As a result, the original pore system of carbonate sediment can become drastically altered prior to burial, such that reservoir properties may not be predictable from facies models alone. The Miocene Santanyí Limestone Formation, Mallorca, Spain, is well exposed and has undergone minimal burial and therefore presents an excellent opportunity to integrate sedimentology, facies architecture, and diagenesis to determine how porosity evolves within individual facies in the shallow subsurface. From here, the impact on pore type, pore volume, pore connectivity, and petrophysical anisotropy can be assessed. The Santanyí Limestone consists of pale mudstones and wackestones, rooted wacke-packstones, stratiform laminites, and skeletal and oolitic, cross-bedded grainstone. Thin-section analysis reveals a paragenetic pathway of grain micritization, followed by dissolution of aragonite, possibly by meteoric fluids associated with karstification. Subsequently, the unit underwent fracturing, compaction, recrystallization, cementation, dolomitization, and matrix dissolution to form vugs. Petrophysical analyses of 2.54-cm-diameter plugs indicate that these complex diagenetic pathways created petrophysical anisotropy [mean horizontal permeability (Kh)/vertical permeability (Kv) of whole formation = 3.4] and that measured parameters cannot be related directly to either geological facies or pore type. Instead, petrophysical data can be grouped according to the diagenetic pathways that were followed after deposition. The best reservoir quality (i.e., typical porosity 15 to >40% and permeability >100 mD) is associated with pale mudstones, stratiform laminites, and skeletal and oolitic grainstone that have undergone pervasive recrystallization or dolomitization. These rocks have the some of the lowest formation resistivity factor (FRF) values (<200) and thus the simplest pore system. The poorest reservoir properties ( k <10 mD) occur in mudstones and wackestones that have not been recrystallized and, hence, are dominated by a simple network of micropores (FRF <101). Skeletal and oolitic grainstones and rooted and brecciated wacke-packstones that have undergone some cementation and partial recrystallization have moderate reservoir properties and a high FRF (>>1000), reflecting a complex pore system of biomolds, vugs, and microporosity. Consequently, reservoir properties can be predicted based on their primary rock properties and the diagenetic pathway that they followed after deposition.