A novel methodology is proposed to characterize coherent structures in large eddy simulations. Based on two passive tracers emitted respectively at the surface and at cloud top, the object‐oriented framework allows individual characterization of coherent tridimensional plumes within the flow. Applying this method in a simulation of the diurnal cycle of a marine stratocumulus‐topped boundary layer shows that coherent updraft and downdraft structures contribute to most of the total transport of heat and moisture, although covering a small part of the domain volume. On average, downdrafts contribute equally compared to updrafts for moisture fluxes and more than updrafts for heat fluxes. The relative contribution of updraft and downdraft objects to heat transport exhibits a large diurnal cycle, which suggests cloud‐turbulence‐radiation interaction. Our results suggest that subgrid downdraft properties within stratocumulus‐topped boundary layers should be represented through nonlocal mass‐flux parameterization in climate models.