Misidentifying spatial population structure may result in harvest levels that are unable to achieve management goals. We developed a spatially explicit simulation model to determine how biological reference points differ among common population structures and to investigate the performance of management quantities that were calculated assuming incorrect spatial population dynamics. Simulated reference points were compared across a range of population structures and connectivity scenarios demonstrating the influence of spatial assumptions on management benchmarks. Simulations also illustrated that applying a harvest level based on misdiagnosed spatial structure leads to biased stock status indicators, overharvesting, or foregone yield. Across the scenarios examined, incorrectly specifying the connectivity dynamics (particularly misdiagnosing source-sink dynamics) was often more detrimental than ignoring spatial structure altogether. However, when the true dynamics exhibited spatial structure, incorrectly assuming panmictic structure resulted in severe depletion if harvesting concentrated on more productive population units (instead of being homogeneously distributed). Incorporating spatially generalized operating models, such as the one developed here, into management strategy evaluations will help develop management procedures that are more robust to spatial complexities.