Proper targeting of the aquaporin-2 (AQP2) water channel to the collecting duct apical plasma membrane is critical for the urine concentrating mechanism and body water homeostasis. However, the trafficking mechanisms that recruit AQP2 to the plasma membrane are still unclear. Snapin is emerging as an important mediator in the initial interaction of trafficked proteins with target-SNARE (t-SNARE) proteins, and this interaction is functionally important for AQP2 regulation. We show that in AQP2-MDCK cells subjected to adenoviral-mediated expression of both snapin and syntaxins, the association of AQP2 with both syntaxin-3 and syntaxin-4 is highly enhanced by the presence of snapin. In pulldown studies, snapin detected AQP2, syntaxin-3, syntaxin-4 and SNAP23 from inner medullary collecting duct. AQP2 transport activity, as probed by AQP2's urea permeability, was greatly enhanced in oocytes that were co-injected with mRNAs of SNARE components (snapin + syntaxin-3 + SNAP23) over those injected with AQP2 cRNA alone. It was not enhanced when syntaxin-3 was replaced by syntaxin-4 (snapin + syntaxin-4 + SNAP23). On the other hand, the latter combination significantly enhanced the transport activity of the related AQP3 water channel while the presence of syntaxin-3 did not. This AQP/syntaxin interaction agrees with the polarity of these proteins' expression in the inner medullary collecting duct epithelium. Thus, our findings suggest a selectivity of interactions between different aquaporin and syntaxin isoforms, and thus in the regulation of AQP2 and AQP3 activities in the plasma membrane. Snapin plays an important role as a linker between the water channel and the t-SNARE complex leading to the fusion event, and the pairing with specific t-SNAREs is essential for the specificity of membrane recognition and fusion.