The pearl oyster (Pinctada maxima) aquaculture industry in the Kimberley region of Western Australia has been established for decades. However, investigation of benthic sediments and macrobenthic communities within pearl farms for this region has not taken place until now. Pearl oysters may have the potential to foul the benthic layer under the farms through the deposition of feces and pseudo-feces from the cultured oysters and fouling organisms, and the fallout of debris from the longlines that suspend the pearl oysters. This organic waste and debris can accumulate in the sediments below the oyster longlines and potentially lead to organic enrichment and even eutrophication. Other aquacultures (such as some finfish and other shellfish) have caused eutrophication of marine sediments and a concurrent change in benthic macrofauna. For two years we sampled the sediments below three P. maxima pearl oyster farms in remote regions of the Kimberley coast. Sediment core samples were taken to measure physico-chemical variables (redox potential, nutrients loads and total organic matter) while grab samples collected the benthic macrofauna (> 1 mm in size). Each farm was compared to four control locations (total = 12 control locations) within the same region. At all three pearl farms there was no indication of eutrophication (nutrient enrichment). We concluded that the variability in benthic physico-chemistry beneath pearl farms was within the bounds of natural variability at reference locations. There were also no consistent differences in the benthic macrofauna assemblages below the pearl oyster farms when compared to control locations. There was considerable natural variability of the benthic macrofauna among all locations, but especially among the reference locations. The reference locations were as different from one another as they were from the farm locations, indicating that the diversity of benthic macrofauna taxa, and their relative abundances within sediments underlying the farms fell within the range of natural variability found at these spatial scales. The importance of robust assessment of potential environmental impact of aquaculture facilities is stressed.