The oceanographic community routinely uses anisotropy of magnetic susceptibility to identify deformation associated with sediment core collection and sampling, as well as to reconstruct primary and post-depositional conditions. These measurements are also applicable to lacustrine settings. Using anisotropy of magnetic susceptibility, in combination with geochemical and physical analyses of lake sediments, permits differentiation of primary depositional conditions from sediment disturbance associated with post-depositional processes and core collection. Detailed analysis of piston cores from Seneca Lake and Owasco Lake, New York (USA) revealed evidence for relatively weak anisotropies that resulted from normal lacustrine sedimentation since ~ 16.8–16.6 cal ka BP. A middle to late Holocene lowstand and associated erosional unconformity was inferred in both lakes using the magnitude of the anisotropy, changes in lithofacies, and increase in % sand. Anomalous magnetic fabrics were also preserved in post-glacial sediment that resulted from core collection and subaqueous slides. Stratigraphic disruptions (“flow-ins”) that formed during coring were recognized by vertically oriented laminae or soupy sediment near the base and top of cores, respectively, and confirmed the rationale for using magnetic fabric measurements. Mid-core “flow-ins” throughout the uppermost 1–2 m of three of the four cores in this study could only be identified by a gradual shift in the dominant shape of the magnetic fabric. Imperfect piston coring likely resulted in vertical strain that produced overthickened sections without destroying the stratigraphic integrity of these sediments. Subaqueous slides were recognized in Owasco Lake by abrupt changes in lithofacies and magnetic fabric. Anisotropy of magnetic susceptibility proved to be a powerful tool to assess lacustrine core integrity in massive and laminated sediment prior to paleoenvironmental reconstruction.