Quantitative models for marine ecosystem-based management are often constrained by availability of observations. Uncertainty about the underlying system structure can affect model estimates and conclusions about the consequences of management actions. Qualitative models can augment model development for decision-making and may provide an alternative to quantitative assessments. We apply qualitative loop analysis to assess the sensitivity of management outcomes to structural uncertainty within the Georges Bank social–ecological system. Loop analysis uses defined positive or negative relationships between system components to provide inference about cascading effects of pressures on components of management interest. We compare the sensitivity of outcomes from two management strategies in four model structures of the Georges Bank system that investigate trophic and socioeconomic model uncertainty. We summarize system responses to perturbation and compare these responses with a set of management objectives. Models with complex socioeconomic structure estimated positive outcomes more often but with less reliability than simpler models. Our analyses demonstrated trade-offs among habitat objectives for two management strategies, as well as uncertainty about the reliability of outcomes, contingent on model structure.