A single-step chemical strategy allows the formation of single-walled carbon nanotube (SWCNT) molecular junctions in aqueous solution. SWCNTs were first wrapped with DNA to be water soluble and solution processable. Diazonium salts, which have been shown to react spontaneously with carbon nanotubes in water at room temperature, were then employed to covalently link SWCNT segments. The DNA wrapping of the nanotubes acted as a protective layer that limits the functionalization predominantly to the nanotube terminal ends, therefore allowing the assembly of linear SWCNT junctions. Upon increasing the concentration of the linker, we observed first the formation of side-to-end junctions, and eventually the assembly, through side-to-side interactions, of SWCNTs into bundles. This approach demonstrates the possibility of tuning the formation of linear and branched carbon nanotube junctions that in turn is of importance for the sustainable fabrication of solution-processable CNT-based nanoscale systems and devices.