The effect of experimental factors [pH and Hg(II)] on the fluorescence excitation emission matrices (EEMs) of nanosensor carbon dots (CDs) was analyzed by multiway decomposition methods based on parallel factor (PARAFAC) analysis. PARAFAC analysis of the EEM structures identifies three components corresponding to two different-sized CDs with the Hg(II) and pH profiles highly correlated plus a background. Parallel profiles with Linear Dependences (PARALIND) model with three components in the excitation–emission spectral modes and two components in the Hg(II) or pH mode gave similar results as PARAFAC, but is more useful from a theoretical point of view because PARALIND shows that the two different-sized CDs have similar chemical reactivity toward Hg(II) and pH. PARAFAC2 was used as a trilinear confirmatory test of the data structures under analysis. Copyright © 2010 John Wiley & Sons, Ltd.