Census counts of benthic foraminifera were studied from the SW Iberian Margin to reconstruct past changes in deep-water hydrography across Terminations I and II. Detailed benthic faunal data (> 125 μm size-fraction) allow us to evaluate the limitations imposed by taphonomic processes and restricted size-fractions. The comparison of recent (mudline) and fossil assemblages at IODP Site U1385 indicates the quick post-mortem disintegration of shells of astrorhizoid taxa (~ 80% of the present-day fauna), resulting in impoverished fossil assemblages. While the application of quantitative proxy methods is problematic under these circumstances, the fossil assemblages can still provide a qualitative palaeoenvironmental signal that, while most fully expressed in the 125–212 μm size-fraction, is nonetheless also expressed to some degree in the > 212 μm size-fraction.