Ecological predictions and management strategies are sensitive to variability in model parameters as well as uncertainty in model structure. Systematic analysis of the effect of alternative model structures, however, is often beyond the resources typically available to ecologists, ecological risk practitioners, and natural resource managers. Many of these practitioners are also using Bayesian belief networks based on expert opinion to fill gaps in empirical information. The practical application of this approach can be limited by the need to populate large conditional probability tables and the complexity associated with ecological feedback cycles. In this paper, we describe a modeling approach that helps solve these problems by embedding a qualitative analysis of sign directed graphs into the probabilistic framework of a Bayesian belief network. Our approach incorporates the effects of feedback on the model's response to a sustained change in one or more of its parameters, provides an efficient means to explore the effect of alternative model structures, mitigates the cognitive bias in expert opinion, and is amenable to stakeholder input. We demonstrate our approach by examining two published case studies: a host–parasitoid community centered on a nonnative, agricultural pest of citrus cultivars and the response of an experimental lake mesocosm to nutrient input. Observations drawn from these case studies are used to diagnose alternative model structures and to predict the system's response following management intervention.