In the last 20 years, both public and private expenditures on resource conservation and environmental protection have increased dramatically. However, there are numerous technical and political barriers to the efficient use of conservation funds. This paper discusses some of these barriers and approaches to overcoming them. It argues that ecosystem complexities such as threshold effects, ecosystem linkages, and spatial connections often mitigate against politically palatable criteria for resource allocation. Ignoring these complexities is likely to result in substantial efficiency losses. While challenges are daunting for the efficient management of conservation investments, payoff is potentially high for the use of sciences.