Ecosystem-scale networks of marine protected areas (MPAs) are important conservation tools, but their effectiveness is difficult to quantify in a time frame appropriate to species conservation because of uncertainties in the data available. The dugong (Dugong dugon) is a mobile marine species that occurs in shallow inshore waters of an ecosystem-scale network of MPAs (the Great Barrier Reef World Heritage Area [GBRWHA]). We developed a rapid approach to assess risk to dugongs in the region and evaluate options to ameliorate that risk. We used expert opinion and a Delphi technique to identify and rank 5 human factors with the potential to adversely affect dugongs and their sea grass habitats: netting, indigenous hunting, trawling, vessel traffic, and poor-quality terrestrial runoff. We then quantified and compared the distribution of these factors with a spatially explicit model of dugong distribution. We estimated that approximately 96% of habitat of high conservation value for dugongs in the GBRWHA is at low risk from human activities. Using a sensitivity analysis, we found that to decrease risk, commercial netting or indigenous hunting had to be reduced in remote areas and the effects of vessel traffic, terrestrial runoff, and commercial netting had to be reduced in urban areas. This approach enabled us to compare and rank risks so as to identify the most severe risks and locate specific sites that require further management attention.