Knowledge of the dynamic changes in molecular size of natural colloidal organic matter (COM) along the aquatic continuum is of vital importance for a better understanding of the environmental fate and ecological role of dissolved organic matter and associated contaminants in aquatic systems. We report here the pH- and cation-dependent size variations of COMs with different sources (river and lake) quantified using flow field-flow fractionation (FIFFF), fluorescence spectroscopy and parallel factor analysis (PARAFAC), attenuated total reflectance Fourier transform infrared (ATR–FTIR) spectroscopy, and zeta potential analysis. Increasing pH caused a decline in molecular sizes and an obvious size transformation from the >10 kDa to 5–10 kDa and further to 1–5 kDa size fraction, whereas the opposite trend was observed for increasing cation (e.g., Ca2+and Cu2+) abundance. Compared with lakewater COM, the riverwater COM exhibited a greater pH-dependent dispersion but less extent in cation-induced aggregation, demonstrating that the dispersion and aggregation dynamics were highly dependent on COM source and solution chemistry (e.g., pH and cations). Based on ATR–FTIR analysis, the extensive dissolution of C=O and C–O functional groups resulted in a greater pH-dependent dispersion for river COM. Fluorescence titration revealed that, despite their similar cation-induced aggregation behavior, the binding constants of all the PARAFAC-derived components for Cu2+were 1–2 orders of magnitude higher than those for Ca2+(logKM: 4.54–5.45 vs. 3.35–3.70), indicating a heterogeneous nature in cation-DOM interactions. The greater extent of decline in zeta potential for lake COM suggested a Ca-induced charge neutralization and aggregation mechanism. However, for Cu-induced aggregation, chemical complexation was the predominant pathway for the river COM, with higher binding constants, while charge neutralization and chemical complexation co-induced the aggregation of lake COM. Thus, natural COMs may have different environmental behavior along the aquatic continuum and further affect the fate and transport of contaminants in aquatic environments.