The growing usage of nanomaterials is causing emerging concern regarding their environmental behavior in aquatic environments. A major need is the capability to detect and quantify nanomaterials in complex water matrices. Carbon60 fullerene is of special interest because of the widespread application of nanocarbon technology. The present study focuses on how to separate and concentrate fullerenes from water containing salts and organic matter and then quantify their concentrations using liquid chromatography coupled with mass spectrometry (LC/MS). The stable aqueous C60 aggregates (nC60) prepared in the present study were approximately 60 to 70 nm in diameter and had an ultraviolet (UV) extinction coefficient of 0.0263 L/mg-cm at 347 nm, which equated to a UV detection limit of 0.4 mg/L based upon an absorbance of 0.01 cm−1. Ultraviolet analysis is not applicable to use in waters containing salts or organics (e.g., tap water) because of their interferences and potential to aggregate nC60 The LS/MS analysis detected C60 as single fullerene rather than aggregates. Three techniques were developed to separate and concentrate nC60 from ultrapure and tap water into toluene to facilitate LC/MS determination: Evaporation of sample to dryness; extraction using 20% NaCl into toluene; and solid-phase extraction. The first two methods had limitations for use in complex water matrices, but aqueous nC60 concentration as low as 300 ng/L in water were quantified using solid-phase extraction (SPE) separation method. This is the first publication on the application of extraction methods for nC60 from ultrapure and tap waters and determination of detection limits by LC/MS.