Mixing caused by the solitary internal waves or solitons in stratified coastal waters is a primary cause of sediment resuspension and transport. Theoretical, experimental, and modeling studies of solitons have focused on nonlinear wave dynamics to explain their main features. However, the 3D cascade of energy from breaking internal wave solitons to turbulence and mixing in the wave induced wake has received less attention. Observations on the California shelf with a spatially distributed fiber optic sensing system revealed coherent structures in the wake of solitary internal waves breaking on the continental slope1,2. Here, we reproduced this phenomenon with a computational fluid dynamics model. The model demonstrated that the coherent structures in the wake of the breaking solitary internal wave are counterrotating helices. The concept of helicity3 as a topological invariant and a measure of the lack of mirror symmetry of the flow can explain the helical nature of these coherent structures4. Both observational and modeling results are consistent with this theoretical conjecture. These coherent structures have a substantial effect on the sediment transport in the bottom boundary layer, formation of nepheloid layers5, and nutrient fluxes.