AbstractWe present the first analysis of frame‐indifferent (objective) fluxes and material vortices in Large Eddy Simulations of atmospheric boundary layer turbulence. We extract rotating fluid features that maintain structural coherence over time for near‐neutral, transitional, and convective boundary layers. In contrast to traditional analysis of coherent structures in turbulent boundary layers, we provide the first identification of vortex boundaries that are mathematically defined to behave as tracer transport barriers. Furthermore, these vortices are indifferent to the choice of observer reference frame and can be identified without user‐dependent velocity field decompositions. We find a strong agreement between the geometric qualities of the coherent structures we extract using our new method and classical descriptions of horizontal rolls and convective cells arising from decades of observational studies. We also quantify trends in individual vortex contributions to turbulent and advective fluxes of heat under varying atmospheric stability. Using recently developed tools from the theory of transport barrier fields, we compare diffusive momentum and heat barrier fields with the presence of rolls and cells, and determine a strong connection between heat and momentum orthogonality with the physical drivers of roll‐cell transformation. This newly employed frame‐indifferent characterization of coherent turbulent structures can be directly applied to numerical model output, and thus provides a new Lagrangian approach to understand complex scale‐dependent processes and their associated dynamics.