Atmospheric pressure photoionization (APPI) was evaluated for the analysis of fullerenes. An important response improvement was found when using toluene mediated APPI in negative mode if compared with other API sources (electrospray and atmospheric pressure chemical ionization). Fullerene APPI negative mass spectra were dominated by the isotopic cluster of the molecular ion, although isotopic patterns for M+1, M+2 and M+3 ions showed higher than expected relative abundances. These discrepancies are explained by the presence of two isobaric ions, one due to 13C and the other to the addition of hydrogen to a double bond of the fullerene structure. Triple quadrupole tandem mass spectrometry and ultra-high resolution mass spectrometry and accurate mass measurements were used to confirm these assignments. Additionally, cluster ions M+16 and M+32 were characterized following the same strategy. Ions due to the addition of oxygen and alkyl additions were attributed to the presence of methanol in the mobile phase. For the fast chromatographic separation of fullerenes (less than 3.5 min) a sub-2 µm C18 column and isocratic elution (toluene:methanol 45:55 v/v) was used. Highly selective-selected ion monitoring (H-SIM) mode (mass resolving power >12,500 FWHM) was proposed monitoring the two most intense isotope ions in the [M]-¿ cluster. Method limits of quantitation down to 10 pg L-1 for C60 and C70 fullerenes and between 0.75-5.0 ng L-1 for larger fullerenes were obtained. Finally, the UHPLC-APPI-MS method was used to analyze fullerenes in river and pond water samples.