Provided herein are methods for making water-soluble nanoparticles comprising a core/shell nanocrystal that is coated with a surface layer comprising enough hydrophilic ligands to render the nanoparticle water soluble or water dispersable. Methods for crosslinking molecules on the surface of a nanoparticle, which methods can be used on the above water-soluble nanoparticles also are provided. Nanoparticle compositions resulting from these methods are also provided.