Decisions about the allocation of conservation resources are often made with a focus on individual species. The management of any one species is, however, likely to impact other species in an ecosystem. For example, the re-establishment of wolves in Yellowstone National Park had dramatic and unexpected indirect impacts on vegetation and water flows via the wolves’ predation on elk. Considering individual species in isolation when making conservation management decisions may be detrimental not only to non-focal species in the system, but also ultimately to the very species we are aiming to protect. A decade or more of food web theory highlights the potential catastrophic cascading impacts of ecosystem modification and collateral impacts have been well documented for the introduction of invasive species. Predicting these ecosystem-level outcomes is notoriously difficult because they depend on accurate and quantitative understanding of the ecosystem dynamics. However for the majority of ecosystems information on these interactions are at best limited and in most cases unknown. In this talk I will present a novel modelling approach using generalized Lotka-Volterra equations to model the uncertain, coupled dynamics of a large system of species and to predict plausible ecosystem models using ‘backcasting’ and limited quantitative or qualitative system observations. I will then explore our ability to understand the potential adverse outcomes from planned management interventions and to inform effective monitoring to detect adverse species responses and hence guide strategic mitigation actions. I will illustrate this work with two Australian case studies, the impacts of cat eradication of Christmas Island, and the risk of perverse outcomes from reintroductions into Booderee National Park.