Water-soluble quantum dots (qdots) have been introduced as bright fluorophores into life sciences research. Although various photophysical pathologies of qdots have been found, how their biological applications will be affected --- particularly in the native biological environment --- has not been evaluated. By fluorescence coincidence analysis and fluorescence cross-correlation spectroscopy, we studied the dark fraction of free-diffusing qdots in aqueous solution. We were able to detect individual qdots and found significant heterogeneity --- well-distinguished dark qdots and bright qdots. We estimated the bright fraction of Qdot525-Streptavidin to be about 55%. Blinking events were also noticed in fluorescence coincidence analysis, with “on/off” timescale from submilliseconds to tens of milliseconds.