The present invention provides for detection apparatus with functionalized fluorescent nanocrystal compositions and methods for making and using these compositions in biological detection applications, material separations, and in the production of biosensors. The compositions are fluorescent nanocrystals coated with at least one coating material comprising ligands with functional groups or moieties with conjugated electrons and moieties for imparting solubility to fluorescent nanocrystals in aqueous solutions. The coating material provides for functionalized fluorescent nanocrystal compositions which are water soluble, chemically stable, and emit light with a high quantum yield and/or luminescence efficiency when excited with light. The coating material may also have chemical compounds or ligands with moieties for bonding to target molecules and cells as well as moieties for cross-linking the coating.