A rapid and large injection of isotopically light carbon into the ocean-atmosphere reservoirs is signaled by a negative carbon isotope excursion (CIE) at the Paleocene-Eocene boundary ∼56 m.y. ago. To better understand the extent of ocean warming and acidification associated with the carbon injection we generated elemental and isotopic records of surface and thermocline planktonic foraminifera across the Paleocene-Eocene boundary from an expanded section along the Mid-Atlantic coastal plain, New Jersey (USA). Ocean temperatures (derived from magnesium/calcium paleothermometer) document a lag in thermocline warming relative to surface waters, implying a progressive deepening of the mixed layer in addition to global warming. A similar magnitude of acidification (as recorded by boron/calcium, B/Ca) on the shelf compared with open ocean sites confirms widespread acidification of the surface ocean. An increase in seawater alkalinity after the CIE, as recorded by B/Ca in planktonic foraminifera, likely played an important role in neutralizing the added carbon, possibly minimizing benthic extinction along the shelf.