Dissolved organic matter (DOM) in aquatic ecosystems can bind with heavy metals, which substantially affects the behavior and fate of the metals. However, the binding potential is highly related to the molecular weights and types of the DOM samples. In this study, aquatic DOMs from different ecosystems (i.e., river and lake) were fractionated into low molecular weight (LMW-, <1 kDa) and high molecular weight (HMW-, 1 kDa~0.45 μm) fractions, and the MW-dependent heterogeneities in Cd(II) were investigated by spectral and titration techniques. The results showed that 38.1~40.1% of organic ligands were distributed in the LMW-fraction, with the remaining 59.9~61.9% in the HMW-fraction. Parallel factor analysis identified one tryptophan-, one tyrosine-, and one fulvic-like component from 60 pristine fluorescence spectra. It was noted that the tryptophan- and tyrosine-like components were mainly located in the HMW-fraction, while the fulvic-like components became the predominant organic ligands in the LMW-fraction. Fluorescence titration analysis showed that, with increased metal addition, the intensities of all fluorescent components exhibited an initial rapid decline followed by a gradual decrease or stabilization, demonstrating effective binding of heavy metals with DOMs. The modified Stern-Volmer model further demonstrated that the Cd(II) binding potential (logK_M) of river DOMs was generally lower than that of lake DOMs for each MW fraction. In addition, irrespective of DOM types, the logK_M values decreased with the order of HMW- > Bulk > LMW-, showing obvious MW-dependent heterogeneities in metal binding. This study clearly revealed that the binding properties of heavy metals with natural DOMs were highly dependent on DOM types as well as MWs.