Critical algal blooms in great lakes increase the level of algal organic matters (AOMs), significantly altering the composition of natural organic matters (NOMs) in freshwater of lake. This study examined the AOM's characteristics of Nitzschia palea (N. palea), one kind of the predominant diatom and an important biomarker of water quality in the great lakes of China, to investigate the effect of AOMs on the variation of NOMs in lakes and the process of algal energy. Excitation–emission matrix fluorescence (EEM) spectroscopy, synchronous fluorescence (SF) spectroscopy and deconvolution UV–vis (D-UV) spectroscopy were utilized to characterize AOMs to study the effects of nutrient loading on the composition change of AOMs. From results, it was revealed that the phosphorus is the limiting factor for N. palea's growth and the generation of both total organic carbon and amino acids but the nitrogen is more important for the generation of carbohydrates and proteins. EEM spectra revealed differences in the composition of extracellular organic matter and intracellular organic matter. Regardless of the nitrogen and phosphorus concentrations, aromatic proteins and soluble microbial products were the main components, but the nitrogen concentration had a significant impact on their composition. The SF spectra were used to study the AOMs for the first time and identified that the protein-like substances were the major component of AOMs, creating as a result of aromatic group condensation. The D-UV spectra showed carboxylic acid and esters were the main functional groups in the EOMs, with –OCH3, –SO2NH2, –CN, –NH2, –O– and –COCH3 functional groups substituting into benzene rings.