This paper reports the first application of a combined approach utilizing split-flow thin-cell (SPLITT) separation to size fractionate natural aquatic colloids and particles collected from freshwater samples. No sample preconcentration was performed although some samples were investigated after alteration of the ambient pH. The unfractionated and fractionated samples were analyzed by scanning electron microscopy (SEM), environmental SEM, and 3D excitation emission matrix fluorescence. Qualitative and quantitative results by microscopy indicated that SPLITT produces well-resolved fractionations at appropriate sizes but with some perturbation of the sample. In addition, tryptophan-like fluorescence was shown to be caused by different organic moieties compared with humic-like and fulvic-like fluorescence. Tryptophan-like fluorescence intensity is found mainly in the particulate material but is not pH dependent, while humic- and fulvic-like fluorescence intensities are dependent on pH but not on size. Fulvic-like fluorescence intensity normalized to absorbance, related to fluorescence efficiency and molar mass, varies with size.