Algogenic organic matter (AOM) in eutrophic water has become a critical problem for the sustainable operation of water treatment plants. As AOM is a high-yielding precursor of disinfection by-products (DBPs), its occurrence in water sources intensively raises public attention on the issues of safe and stable supply of drinking water. This chapter presents current advanced knowledge of AOM characterization and their applications for the prediction of DBP formation upon chlorination. Herein, two dominant classes of carbonaceous DBP (C-DBPs), trihalomethanes (THMs) and haloacetic acids (HAAs), were reviewed as major products of DBP from the eutrophic water. Overall, AOM is higher yielding THM and HAA precursors upon chlorination compared to terrestrial natural organic matter (NOM). Of the characterization tools, fluorescent spectrometry, i.e., excitation–emission matrix (EEM), is an advanced proxy to trace AOM-derived C-DBP formation over traditional bulk parameters or ultraviolet absorbance because of its greater sensitivity and selectivity. However, future work may use EEM technique in combination with bulk parameters, such as chlorine consumption, or MW properties to increase its predictability to AOM-DBP formation.