The AND-2A drill hole (ANDRILL [Antarctic Geological Drilling Program] Southern McMurdo Sound Project), ∼10 km from the East Antarctica coastline, records nearly 6 m.y. of sedimentation across the Miocene climatic optimum at a high-latitude site. Sedimentological studies of bedforms and particle size distributions indicate that the paleoenvironment was strongly affected by waves and currents, consistent with deposition in a glacially influenced neritic environment. We document abrupt shifts in mud percent within glacial-interglacial cycles ca. 17.8 Ma and between ca. 16.7 and 15.7 Ma that we attribute to the hydrodynamic effects of wave stirring tied to episodes of ice growth and decay. Although wave climate and geodynamic forcing of the paleobathymetry simultaneously affect wave stirring on a high-latitude shelf, both are ultimately controlled by the size of the ice sheet. The mud percent record displays cyclicity at short-eccentricity time scales (94–99 k.y.) and, unexpectedly, ice retreat phases interpreted from the particle size record coincide with eccentricity minima. We attribute the eccentricity-paced ice retreat phases during the late Early Miocene polythermal glacial conditions and the cool orbital parameters to marine ice sheet instability in response to changes in ocean circulation and heat transport. The particle size record of the AND-2A core provides unique near-field evidence for orbitally paced changes in high-latitude climate and ice volume during the Miocene climatic optimum and important insights into the mechanisms of ice sheet growth and decay in a period of global warmth.