Single-walled carbon nanotubes (SWCNTs) dispersed in aqueous medium have many potential applications in chemistry, biology, and medicine. Reversible aggregation of SWCNTs dispersed in water has been frequently reported, but the mechanisms behind are not well understood. Here we show that SWCNTs dispersed into aqueous medium assisted by various charged molecules can be reversibly aggregated by a variety of electrolytes with two distinct mechanisms. Direct binding of counterions to SWCNTs leads to aggregation when the surface charge is neutralized from 74 to 86%. This aggregation is driven by electrostatic instead of van der Waals interactions, thus showing similarity to that of DNA condensation induced by multivalent cations. Sequestration of counterions by chelating reagents leads to the redispersion of SWCNT aggregates. In contrast to various metal ions, polyelectrolytes have the unique ability to induce SWCNT aggregation by bridging between individual SWCNTs. Aggregation through the latter mechanism can be engineered to be reversible by exploiting various mechanisms of chain breaking, including reduction of disulfide bond in the polymer chain, and the cleavage action of proteolytic enzymes. These findings clarify the mechanisms of SWCNT aggregation, and have broad implications in various applications of SWCNTs in water.