The sequence stratigraphic framework of initiation and growth of carbonates in environments impacted by siliciclastic inputs is highly variable because of the biogenic nature of the sedimentary production and its sensitivity to environmental conditions. Using panorama interpretations, logging, and characterization of benthic communities, the mixed carbonate–siliciclastic sedimentary succession of the Neogene Lorca Basin (SE Spain) has been studied to decipher the role of local and global controlling parameters on the sequence stratigraphic framework of carbonate production. Three different carbonate depositional models are distinguished: 1) retrogradational homoclinal ramps (type 1) dominated by heterozoan communities that developed lateral to alluvial fans, 2) progradational flat-topped coral platforms (type 2) with Porites and Tarbellastraea coral carpets with a coeval retrogradational pattern on basin margins, and 3) retrogradational narrow siliciclastic-rich coral platforms (type 3) with Tarbellastraea buildups intercalated with deltaic deposits. Onset of carbonate production systematically occurred during transgressions controlled by eustasy and was locally enhanced by extensional tectonics. In steep margins located in the vicinity of major marginal faults, transgressions were characterized by high terrigenous inputs, and only heterozoan-dominated ramps (type 1) developed. The flooding of these steep and tectonically active margins characterized by small drainage basins and immature, locally sourced alluvial systems led to lower terrigenous fluxes and the growth of coral flat-topped platforms (type 2) during subsequent highstands. Away from main marginal faults, deltaic environments were sourced by large drainage basins. They were characterized by a flat topography that permitted the occurrence of a shallow photic zone subject to low and irregular terrigenous inputs up to the distal part of the depositional profile during transgressions. In this deltaic configuration, the growth of narrow siliciclastic-rich coral platforms (type 3) were favored. On these platforms, coral buildups were regularly buried by terrigenous inputs during highstands. In the Lorca Basin, the dimensions of siliciclastic systems and the size of their drainage basins also directly impacted the sequence stratigraphic framework of carbonates intercalated in terrigenous units. This study illustrates the marked variability in: 1) the different types of carbonate depositional profiles and 2) the timing of these carbonates in a mixed carbonate–siliciclastic system because of the size, maturity, and location of siliciclastic systems, local tectonics, inherited topography, and global sea-level fluctuations.