Uniaxial order parameters of the nematic and columnar mesophases in the lyotropic chromonic liquid crystal Sunset Yellow FCF have been determined from deuteron nuclear magnetic resonance, where random confinement of the system by the dispersion of aerosil nanoparticles has been performed to help obtain the angular dependent spectra. The long-time evolution study of the order parameters shows that the system requires tens of hours to stabilize after a deep change in temperature, in contrast with the very fast assembly process of the aggregates. Finally, the degree of order of the water molecules, forced by the uniaxial environment, has been determined.