Sephacryl-based separation of single-walled carbon nanotubes (SWCNTs) has afforded the enrichment of samples according to both type (metal/semiconducting) and band structure (chirality). However, Sephacryl-based procedures suffer from low process efficiency, in that some of the purified SWCNTs remain irreversibly bound on the gel. This work focuses on the elucidation of mechanistic aspects relating to the irreversible retention of SWCNT by Sephacryl S200 and identification of strategies to reduce material loss. By probing system parameters such as SWCNT or sodium dodecyl sulfate (SDS) concentration during adsorption, loading ratio (number of SWCNTs vs. number of gel binding sites), and the effect of kosmotropic additives on process elution efficiency, this work identifies inhomogeneous features belonging to SWCNTs as the primary factor which promotes their irreversible retention. Process elution efficiency is found to be negatively correlated with increased SDS surfactant concentration and increased SWNT loading, and methods are identified to mitigate material losses in Sephacryl-based SWCNT separation schemes. Application of NaF, a strong kosmotropic agent, to elute SWCNTs from Sephacryl is found to increase process elution efficiency from 54% to 88% compared to SDS surfactant alone. Collectively, this work both improves upon and provides valuable insight into the purification of SWNT with Sephacryl.