Single-walled carbon nanotubes (SWCNTs) have attracted much attention for applications in biomedical imaging and sensing due to their photostable, environmentally responsive near-infrared fluorescence. Single-stranded DNA was found to non-covalently disperse SWCNTs in water while preserving their optical properties and providing a biocompatible wrapping suitable for cellular interactions. The hybridization of DNA-SWCNTs has been studied extensively to determine the relationship between oligonucleotide sequence and SWCNT properties in situ, however intracellular environments introduce harsh conditions that can change the identity of the hybrid nanomaterial, altering its intrinsic optical properties. Aggregation via protein-nanotube interactions adds complexity to the biological system, while also causing concerns for cellular toxicity. Here, we show that the stability of DNA-SWCNTs after internalization by mammalian cells is dependent upon the oligonucleotide sequence that wraps the nanotube. The relationship between sequence length, fluorescence stability, and uptake are examined to provide insight on intracellular mechanisms that require considerations in nanotube sensor design. We show that aggregation not only alters the expected rate of uptake into the cells but further affects the endosomal processing pathways. We propose a model for the uptake and expulsion of SWCNTs that accounts for the aggregation state and DNA wrapping. These findings provide fundamental understanding of the interactions between nanotubes and live cells which can be applied towards development of carefully engineered carbon nanotube sensors.