Nanoparticles described as metal-encapsulated carbonaceous dots or M@C-dots are disclosed. Also disclosed are specific M@C-dots with gadolinium, so called Gd@C-dots. These nanoparticles are biologically inert and preclude the release of metal in biological environments. In addition, despite a dimension exceeding the commonly recognized threshold for renal clearance, the disclosed nanoparticles can be efficiently cleared via urine after systematic injection. Methods of making and using such nanoparticles are also disclosed.