The dataset comprises catch records of infauna from box core deployments completed on research voyage SS 03/2005. The survey design was a natural experiment (i.e. control-impact, but not before-after) to test the long-term, broadscale effects of prawn fishing on non-target species and habitats. Deployments were stratified by fishing intensity (three strata) and day/night. The survey was repeated in three regions: (a) north of Groote Eylandt, (b) north-east of the Vanderlins, and (c) north of Mornington Island. The number of deployments completed as part of the natural experiment was 123.