We developed a population model of magpie geese in the Northern Territory that considered spatial and temporal variation and related sources of uncertainty, building on previous analyses of the plausible rates of increase for this species. The model was used to explore realistic limits to recreational and indigenous harvest and to examine productive, yet risk-averse, management regimes for long-term sustainability. Harvest strategies based on a proportional off-take provided similar yields to a fixed quota system, but resulted in a reduced risk of substantial population decline. Moreover, higher harvests could be supported in model systems that incorporated dispersal phenomena consistent with patterns suggested by the observed distributional and abundance patterns. However, irrespective of harvest strategy and spatial structure, off-take at the levels implied in previously published analyses are clearly unsustainable. These results illustrate the desirability of matching the design of management systems to the heterogeneity of population processes. Management regimes that fail to take account of spatial and temporal heterogeneity could damage the interests of important stakeholder groups and potentially imperil the future viability of the species. However, the costs of disaggregated management systems may be substantial and benefits of investment in them need to be clearly demonstrated. Gaining better appreciation of spatial variation in harvests should be given high priority.