Risks from human intervention in the climate system are raising concerns with respect to individual species and ecosystem health and resiliency. A dominant approach uses global climate models to predict changes in climate in the coming decades and then to downscale this information to assess impacts to plant communities, animal habitats, agricultural and urban ecosystems, and other parts of the Earth’s life system. To achieve robust assessments of the threats to these systems in this top-down, outcome vulnerability approach, however, requires skillful prediction, and representation of changes in regional and local climate processes, which has not yet been satisfactorily achieved. Moreover, threats to biodiversity and ecosystem function, such as from invasive species, are in general, not adequately included in the assessments. We discuss a complementary assessment framework that builds on a bottom-up vulnerability concept that requires the determination of the major human and natural forcings on the environment including extreme events, and the interactions between these forcings. After these forcings and interactions are identified, then the relative risks of each issue can be compared with other risks or forcings in order to adopt optimal mitigation/adaptation strategies. This framework is a more inclusive way of assessing risks, including climate variability and longer-term natural and anthropogenic-driven change, than the outcome vulnerability approach which is mainly based on multi-decadal global and regional climate model predictions. We therefore conclude that the top-down approach alone is outmoded as it is inadequate for robustly assessing risks to biodiversity and ecosystem function. In contrast the bottom-up, integrative approach is feasible and much more in line with the needs of the assessment and conservation community. A key message of our paper is to emphasize the need to consider coupled feedbacks since the Earth is a dynamically interactive system. This should be done not just in the model structure, but also in its application and subsequent analyses. We recognize that the community is moving toward that goal and we urge an accelerated pace.