Fixed-point and probabilistic sampling designs were compared to investigate which design best detected known contamination gradients in the marine ecosystem adjacent to McMurdo Station, Antarctica. The fixed-point sampling design included transects along historical contamination and physical disturbance gradients. The probabilistic sampling design used randomly selected hexagons spaced at 50 m intervals. In both designs, 15 stations were sampled over a small area (~1 km2) that extended from Winter Quarters Bay to Cape Armitage. Sediment quality triad components (sediment chemical contaminants, sediment toxicity, and a benthic index of biotic integrity) were measured to indicate chemical, toxicological, and biological effects. There were higher correlations between sediment quality triad components for the fixed-point sampling design than for the probabilistic design. The fixed-point design was better at detecting the intensity of alteration because disturbance of the marine ecosystem at McMurdo Station is localized within a small area. Based on these results, a limited fixed-point design with nine stations detected no significant change in macrofaunal community structure over a four year period from 2000–2004. However, the macrofaunal assemblages present in the contaminated portions of Winter Quarters Bay are indicative of a disturbed benthic community that has been subject to organic enrichment and toxic chemical exposure.