Exceptional 3-D exposures of fault blocks forming a 5 km × 10 km clastic sediment-starved, marine basin (Carboneras subbasin, southeast Spain) allow a test of the response of carbonate sequence stratigraphic architectures to climatic and tectonic forcing. Temperate and tropical climatic periods recorded in biofacies serve as a chronostratigraphic framework to reconstruct the status of the basin within three time-slices (late Tortonian–early Messinian, late Messinian, Pliocene). Structural maps and isopach maps trace out the distribution of fault blocks, faults, and over time, their relative motions, propagational patterns and life times, which demonstrate a changing layout of the basin because of a rotation of the regional transtensional stress field. Progradation of early Messinian reefal systems was perpendicular to the master faults of the blocks, which were draped by condensed fore-slope sediments. The hangingwall basins coincided with the toe-of-slope of the reef systems. The main phase of block faulting during the late Tortonian and earliest Messinian influenced the palaeogeography until the late Pliocene (cumulative throw < 150–240 m), whereas displacements along block bounding faults, which moved into the hangingwall, died out over time. An associated shift of the depocentres of calciturbidites, slump masses and fault scarp degradation breccias reflects 500–700 m of fault propagation into the hangingwall. The shallow-water systems of the footwall areas were repeatedly subject to emergence and deep peripheral erosion, which imply slow net relative uplift of the footwall. In the dip-slope settings, erosional truncations of tilted proximal deposits prevail, which indicate rotational relative uplift. Block movements were on the order of magnitude of third order sea-level fluctuations during the late Tortonian and earliest Messinian. We suggest that this might be the reason for the common presence of offlapping geometries in early Messinian reef systems of the Betic Cordilleras. During the late Pliocene, uplift rates fell below third order rates of sea-level variations. However, at this stage, the basin was uplifted too far to be inundated by the sea again. The evolution of the basin may serve as a model for many other extensional basins around the world.