The fundamental processes and controls on carbonate deposition are well established. These include: water depth, temperature, salinity, clarity, and an abundance of sunlight, all of which control rates of growth among the biota while wave and current energy ensure a steady supply of nutrients. The aragonite-dominated systems of the tropical latitudes gave way to calcite dominance in higher latitudes. Mud-rich tidal-flat sequences characterize the Bahamian and Persian Gulf settings, while mud-free systems dominate the higher-energy settings of the Great Barrier Reef and cooler-water environments. With the inclusion of recently documented Lophelia “reef mounds” in deep arctic waters, together with studies of deep-water pelagic limestones, the globalization of carbonates was nearly complete - almost.

One part of the global distribution pattern remains understudied and underappreciated, namely the equatorial belt. In old mariner terminology this latitudinal belt is known as the doldrums, notorious for its unpredictable calms and seasonal monsoon shifts in the wind and surface currents. In recent years, the Indonesia - Philippines archipelago has received particular attention from oceanographers and climatologists in recognition and growing awareness of the role of El Nino Southern Oscillation (ENSO) and the Indonesian Throughflow (ITF) and its relation to upwelling and changes in sea-surface temperature (SST), resulting in widespread reef death throughout the region.

The archipelago straddles the equator and lies squarely within this equatorial belt. Average sea-water temperatures are ∼ 28–30°C, and salinities are much lower than normal, ∼< 32–34%. These values test the tolerance limits of many reef community members, hence their susceptibility to El Niño events. Collision tectonics has defined the structural style, geography, and hydrography of the archipelago since the earliest Tertiary and has profoundly influenced modern and Cenozoic depositional systems. Shifts in relative sea level are frequent and often dramatic, affecting not only depositional patterns but also diagenesis, with repeated subaerial and flooding events.

The symmetry of the seasonal shifts introduces a bimodal pattern while the energy of the system reduces mud accumulation on the shallow platforms. Nearshore fringing reefs are limited by the high clastic discharge associated with high rainfall and landform topography. Coastal plains are clastic dominated, with mangrove swamp peats replacing the microbial mats that typify large tracts of the Bahamian and Persian Gulf platform settings.

Thus, the region offers an excellent opportunity to study modern and ancient carbonate systems under this particular climatic and, perhaps just as importantly, tectonic setting. That almost half of Indonesia’s hydrocarbon reserves and production derive from these same Cenozoic carbonates provides additional reason for further study.