We used cores and logs from Integrated Ocean Drilling Program (IODP) Expedition 313 to generate biostratigraphic, lithofacies, biofacies, and geochemical data that constrain the ages and paleoenvironments of Pleistocene sequences. We integrate sequence stratigraphy on cores with new seismic stratigraphic data to interpret the Pleistocene history of the Hudson shelf valley and paleoenvironmental and sea-level changes on the inner to middle continental shelf. Improved age control compared to previous studies is provided by integrated calcareous nannofossil biostratigraphy, Sr isotopic stratigraphy, and amino acid racemization. We recognize four upper Pleistocene–Holocene sequences: sequence uP1 is correlated with Marine Isotope Chrons (MIC; “chron” is the correct stratigraphic term for a time unit, not “stage”) 7 or 5e, sequence uP2 with MIC 5c, sequence uP3 with MIC 5a, and sequence uP4 with the latest Pleistocene to Holocene (MIC 1–2). However, within our age resolution it is possible that sequences uP2 and uP3 correlate with MIC 4–3c and 3a, respectively, as suggested by previous studies. Lower Pleistocene sequences lP1 and lP2 likely correlate with peak interglacials (e.g., MIC 31 and MIC 45 or 47, respectively). Thus, we suggest that preservation of sequences occurs only during peak eustatic events (e.g., MIC 45 or 47, MIC 31, and MIC 5), unless they are preserved in eroded valleys. The architecture of the Pleistocene deposits at Sites M27 and M29 is one of thin remnants of highstand and transgressive systems tracts, with lowstand deposits only preserved in the thalwegs of incised valleys. Incised valleys at the bases of sequences uP3 (IODP Site M27) and uP2 (IODP Site M29) document more southward courses of the paleo–Hudson valley, compared to the more southeastward course of the MIC 1–2 paleo–Hudson valley. The patchy distribution of Pleistocene sequences beneath the New Jersey inner-middle continental shelf is due to low accommodation during an interval of large eustatic changes; this predicts that sequences in such settings will be discontinuous, patchy, and difficult to correlate, consistent with previous studies in Virginia and North Carolina.