As a result of recent advances by carbonate petrologists and geochemists, hydrologists are provided with new insights into the origin and explanation of many aquifer characteristics and hydrologic phenomena. Some major advances include the recognition that: (1) most carbonate sediments are of biological origin; (2) they have a strong bimodal size-distribution; and (3) they originate in warm shallow seas. Although near-surface ocean water is oversaturated with respect to calcite, aragonite, dolomite and magnesite, the magnesium-hydration barrier effectively prevents either the organic or inorganic formation of dolomite and magnesite. Therefore, calcareous plants and animals produce only calcite and aragonite in hard parts of their bodies. Most carbonate aquifers that are composed of sand-size material have a high initial porosity; the sand grains that formed these aquifers originated primarily as small shells, broken shell fragments of larger invertebrates, or as chemically precipitated oolites. Carbonate rocks that originated as fine-grained muds were initially composed primarily of aragonite needles precipitated by algae and have extremely low permeability that requires fracturing and dissolution to develop into aquifers. Upon first emergence, most sand beds and reefs are good aquifers; on the other hand, the clay-sized carbonate material initially has high porosity but low permeability, a poor aquifer property. Without early fracture development in response to influences of tectonic activity these calcilutites would not begin to develop into aquifers. As a result of selective dissolution, inversion of the metastable aragonite to calcite, and recrystallization, the porosity is collected into larger void spaces, which may not change the overall porosity, but greatly increases permeability. Another major process which redistributes porosity and permeability in carbonates is dolomitization, which occurs in a variety of environments. These environments include back-reefs, where reflux dolomites may form, highly alkaline, on-shore and continental lakes, and sabkha flats; these dolomites are typically associated with evaporite minerals. However, these processes cannot account for most of the regionally extensive dolomites in the geologic record. A major environment of regional dolomitization is in the mixing zone (zone of dispersion) where profound changes in mineralogy and redistribution of porosity and permeability occur from the time of early emergence and continuing through the time when the rocks are well-developed aquifers. The reactions and processes, in response to mixing waters of differing chemical composition, include dissolution and precipitation of carbonate minerals in addition to dolomitization. An important control on permeability distribution in a mature aquifer system is the solution of dolomite with concomitant precipitation of calcite in response to gypsum dissolution (dedolomitization). Predictive models developed by mass-transfer calculations demonstrate the controlling reactions in aquifer systems through the constraints of mass balance and chemical equilibrium. An understanding of the origin, chemistry, mineralogy and environments of deposition and accumulation of carbonate minerals together with a comprehension of diagenetic processes that convert the sediments to rocks and geochemical, tectonic and hydrologic phenomena that create voids are important to hydrologists. With this knowledge, hydrologists are better able to predict porosity and permeability distribution in order to manage efficiently a carbonate-aquifer system.