23Na multiple quantum filtered (MQF) rheo-NMR methods were applied to probe the molecular foundation for flow induced self-assembly in 0.5% κ-carrageenan fluid. This method is sensitive enough to utilize an endogenous sodium ion concentration of approximately 0.02%. Rheo-NMR experiments were conducted at different temperatures and shear rates to explore varying molecular dynamics of the biopolymer in the fluid under shear. The temperature in the rheo-NMR experiments was changes from 288 K to 313 K to capture transition of κ-carrageenan molecules from helices to coils. At each temperature, the fluid was also tested for flow and oscillatory shear behaviour using bulk rheometry methods. It was found that the 23Na MQF signals were observed for the 0.5% κ-carrageenan solution only under shear and when the fluid demonstrated yielding and/or shear-thinning behaviour. At temperatures of 303 K and above, no 23Na MQF signals were observed independent of the presence or absence of shear as the molecular phase transition to random coils occurs and the fluid becomes Newtonian.