The fluorescence emission and excitation emission matrix (EEM) technologies were used to characterize the dissolved organic matter (DOM) in the water body of the Yangtze River and Jialing River around the Chongqing urban areas from April to August 2008. Concerning about the accidents of the Wenchuan’s Earthquake in May and Tangjiashan Yansaihu’s effects in June,and the high water period time in the summer in two months of July and August,from the EEM obtained from each sampling station and time,the composition,distribution and their changing features of the DOM in the two rivers were investigated as combined with the water samples’ environmental parameters such as pH,DO,DOC with EEM’s fingerprint features,f450/500 etc;finally the bio-environment behavior effects of the three types of fluorescence peaks were elaborated,where humic-like,fulvic-like,and protein-like from the five sampling stations’ EEMs during the five months were given detailed representation. From the experimental results obtained,the fluorescence peaks are mainly composed of two types of fluorophores,humic-like and protein-like in the two rivers around the Chongqing urban areas during the investigation in five months,the protein-like’s peaks value in Jialing River is higher than the values in the Yangtze River,and all the fluorescence peaks in the two Rivers’ water body decrease more or less after the two Rivers join in Chun Tan sampling station;the protein-like peak is notably higher after the “5·12” Earthquake period time including May and June and high water period time,which mainly originated from terrestrial sources,but its intensities decreased observably while the water bodies of the two rivers joining together in the Chao Tianmen and Chun Tan’s sampling station.