The analytical high performance size exclusion liquid chromatography (SEC-HPLC) with multi-wavelength absorbance and fluorescence detections and fluorescence 3D-excitation/emission matrix (EEM) were used for the analysis of average molecular size (MS), molecular size distribution of aliphatic/aromatic compounds and fluorophores in dissolved organic matter (DOM) from Suwannee River (SRDOM) and two Karelian lakes (Vodoprovodnoe Lake - L1DOM and Onego Lake - L2DOM). The average MS of DOM samples varied in the order SRDOM L1DOM L2DOM. The absorbance ratios A250/A365 and A210/A254 have been used for the DOM samples characterization. The absorbance ratio A250/A365 provided significant information about average MS of the bulk aquatic DOMs but was not exactly correlated with the results of SEC-HPLC data. The absorbance ratio A210/A254 in combination with SEC was well correlated with the content of DOM aliphatic/aromatic compounds and could be used as an important water quality index to estimate the level of protein-like material in the aquatic DOM. Regardless of the origin (river or lakes), different geographical locations and different average MS of DOM, several similar types of humic-like SEC-separated fluorophores were found within the samples. In all DOM samples the decrease of the fluorophores emission maxima paralleled the decrease of their relative MS. The combination of SEC-HPLC with multi-wavelength fluorescence and absorbance detection and EEM analyses appears very useful for DOM characterization and for tracking of microbial activity resulting from anthropogenic and/or eutrophic impact in aquatic environments.