Ecosystem process measurements were made on sediment sampled with a box core and water sampled from CTD profiles. For sediments, measurements were of wet/dry weight ratio, total organic carbon, chlorophyll and stable isotopes, nitrogen cycling (nitrogen fixation and denitirification) and oxygen demand. For water samples, measurements were of total suspended solids, chlorophyll and stable isotopes. 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.