During the early Pliocene, subaqueous delta‐scale clinoforms developed in the Águilas Basin, in a mixed temperate carbonate–siliciclastic system. The facies distribution is consistent with the infralittoral prograding wedge model. Stacking patterns and bounding surfaces indicate that the clinoforms formed during the highstand and falling sea‐level stages of a high rank cycle. Twenty‐two prograding clinothems were recognized over a distance of ≥1 km. Biostratigraphic data indicate a time span shorter than 700 kyr for the whole unit (MPl3 biozone of the Mediterranean Pliocene). Cyclic skeletal concentrations and occasional biostromes of suspension feeders (terebratulid brachiopods, modiolid bivalves and adeoniform bryozoan colonies), slightly evolved glauconite and occasional Glossifungites ichnofacies formed on the clinoforms during high‐frequency pulses of relative sea‐level rise. During such stages, increased accommodation space in the topsets of the clinoforms caused a strong reduction of terrigenous input into the foresets and bottomsets. This provided favourable conditions for the development of these suspension feeder palaeocommunities. During stillstand stages, however, reduced accommodation space in the topsets eventually resumed progradation in the foresets. There, the abundance of Ditrupa tubes indicates frequent siltation events that extirpated the terebratulid populations and other epifaunal suspension feeders in the foreset and bottomset subenvironments. The occurrence of shell beds on the clinoforms suggests that this case study represents lower progradation rates than standard examples where shell beds bound the clinobedded units at their base and top only. Importantly, the distributions of biofacies and ichnoassemblage associations contribute significantly to the understanding of the effects of relative sea‐level fluctuations on the evolution of subaqueous delta‐scale clinoform systems.