Self-assembly of aliphatic as well as aromatic thiol-terminated molecules was achieved onto a variety of gold surfaces using aqueous micellar solutions. Scanning tunneling microscopy experiments allowed us to demonstrate that the increase in the density of self-assembled monolayers (SAMs) prepared from micellar aqueous solvent compared to that prepared from ethanol directly originates from the decrease in defect density in the SAM (etch pits, domain boundaries) and not from a denser local packing of the molecules. Extending the use of such an aqueous solvent to various conjugated molecules, we report for the first time the insertion of these molecules from an aqueous solution in a dodecanethiol (DT) SAM and the ligand-exchange on the surface of DT stabilized gold nanoparticles deposited as a Langmuir-Blodgett film. Finally, we show that aqueous micellar DT solutions allow the preparation of DT SAMs on gold through a micropatterned resist mask. These results make possible the use of water to deliver molecules on a solid substrate to build molecular devices in a way compatible with lithography requirements in microelectronic processes.