Benthic foraminifera of box core and piston core samples were collected from the Amazon middle to outer shelf. The assemblages and their taphonomic features confirmed a record of oceanographic changes from the early Holocene to the present. Foraminiferal data in conjunction with sedimentological, stratigraphic, seismic, and isotopic results point to three contrasting depositional environments. The first environment is that of a fluid mud with silt and organic laminations. A seismic discontinuity was observed and interpreted as an erosional surface between the fluid mud, and an underlying much denser mud. This fluid mud, deposited during the last 100 years, shows a very high sedimentation rate, with the erosional phase lasting for 700 years. The characteristic species of the dominant Ammonia beccarii Pseudononion atlanticum assemblage are opportunistic at the sediment-water interface. At deeper substrate intervals, the assemblage can be matched with that at the sediment-water interface, but they also show taphonomic effects of reworking and erosion. The second environment is characterized by relict sediment, which includes an older suite of foraminifera mixed with modern tests. This assemblage differs from the recent one by including large relict species dominated by Quinqueloculina bicostata, Q. lamarckiana, Amphistegina lessonii and Eponides repanda. Two hypotheses account for the relict assemblage: periods of low sea-level and mixing with younger sediments in deeper water. The third environment is in front of the Amazon River mouth. The cores taken here contain abnormal, large tests of Flintina bradyana. The strong currents and tides of the Amazon shelf could cause large tests to move along the seabed by bed-load transport processes. In living foraminifera, such tests may break and later regenerate abnormally. Such occurrences vary stratigraphically and geographically, demonstrating hydrodynamic variations in time and space.