The terminal carbonate complex of southeast Spain is a Miocene (Messinian) unit of oolite, microbialite, and coralgal reefs deposited in association with glacioeustasy and evaporitic drawdown. The relationship between paleotopography and sea level history is useful for prediction of microbialite and oolite reservoir fades in the subsurface. Four sequences record sea level change with minimum amplitudes of 32-77 m (105-253 ft). Sequences commonly have local basal stromatolites overlain by local thrombolites, ooid grainstone, volcaniclastic-rich planar-bedded ooid grainstone, and fenestral ooid grainstone. At low substrate positions, thrombolite boundstones are thicker and laterally more continuous than at higher positions. At intermediate substrate positions (relative to sea level history), sequences have a build-and-fill architecture, characterized by a relief-building phase and a relief-filling phase, with thin sequences draping paleotopography. Microbialites dominate during the relative sea level rises and build topographic relief. Oolites dominate during the relative sea level falls and fill topographic relief. At higher substrate positions, close to highstand, sequences thicken and yield stratigraphic character that is inconsistent with a build-and-fill model. Apparently, the build-and-fill model requires an intermediate-elevation substrate position and nonoptimal carbonate productivity during rapid sea level change. Sequences progressively show increasing diversity and more normal marine organisms, possibly caused by decreasing aridity. Lithofacies of the La Molata area show evidence of more restricted conditions compared to the La Rellana-Ricardillo area lithofacies, likely because La Molata was in an embayment. These results show that distribution of oolite, microbialite, and reef fades are predictable given known interaction among sea level, paleotopography of the depositional surface (substrate), and coastline configuration.