Integrated Ocean Drilling Program (IODP) Expedition 313 drilled three holes (Sites M27, M28, and M29; 34–36 m present water depth) across a series of prograding clinothems from the inner continental shelf of the New Jersey (USA) margin, a region that is sensitive to sea-level change. We examined 702 late Eocene to Miocene samples for benthic foraminiferal assemblages and planktonic foraminiferal abundances. We integrate our results with lithofacies to reconstruct paleobathymetry. Biofacies at all three sites indicate a long-term shallowing-upward trend as clinothems built seaward and sediment filled accommodation space. Patterns in biofacies and lithofacies indicate shallowing- and deepening-upward successions within individual sequences, providing the basis to recognize systems tracts, and therefore sequence stratigraphic relationships in early to early-middle Miocene sequences (ca. 23–13 Ma). The clinothem bottomsets and the lower portions of the foresets, which contain the thickest parts of clinothems, yield the deepest water biofacies. Shallower biofacies characterize the sequences in the upper portions of the clinothem foresets and on the topsets. Topsets are characterized by transgressive (TST) and highstand systems tracts (HST). Foresets contain lowstand systems tracts (LST), TSTs, and HSTs. Flooding surfaces mark parasequence boundaries within LSTs, TSTs, and HSTs. Superimposed on the long-term trends, short-term variations in paleowater depth are likely linked to global sea-level changes indicated by global oxygen isotopic variations.