We report a simple one-pot strategy to prepare surface-function-alized, water-dispersible iron oxide nanoparticles. Small organic molecules that have desired functional groups such as amines, carboxylics, and thiols are chosen as capping agents and are injected into the reaction medium at the end of the synthesis. A diversity of functionalities are effectively introduced onto the surface of the nanoparticles with a minimal consumption of solvents and chemical resources by simply switching the capping ligand to form the ligand shell. The resulting nanocrystals are quasi-spherical and narrowly size-distributed. Energy-dispersive X-ray analysis and Fourier transform infrared spectroscopy studies suggest a successful surface modification of iron oxide nanoparticles with selected functionalities. The colloidal stabilities are characterized by dynamic light scattering and zeta potential measurements. The results imply that functionalized nanoparticles are very stable and mostly present as individual units in buffer solutions. The pedant functional groups of the capping ligand molecules are very reactive, and their availabilities are investigated by covalently linking fluorescent dyes to the nanoparticles through the cross-linking of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride. The quenched quantum yield and shortened lifetime of the dyes strongly indicate a direct bonding between the functional group of the nanoparticles and the fluorescent molecules.