In order to reveal the sources, compositions, distributions and vertical distribution characteristics of endogenous pollutants in lake sediments, the ultraviolet-visible spectroscopy and three-dimensional fluorescence spectrum technology were applied to study the spectral characteristics. Data used in this work including sediment samples collected from the original riverbed, the newly submerged bottom and the newly submerged edge along the lakeside from the newly-built artificial deep-water lake, Lake Longjing. The divisive criterion of sampling sites is the main applications of those lands before impoundment. Results show that the aromaticity and humification of dissolved organic matter (DOM) in pore water is higher than those of overlying water. The proportion of hydrophobic components in pore water is greater than that in overlying water, which means there might be internal input of low molecular weight DOM. Data indicates that DOM of each sample mainly come from aquatic microbial activity within the water body and newly-released organic matter might exist. DOM of overlying water and pore water in Lake Longjing sediments mainly include humic-like parts and protein-like parts with humic-like peaks detected in the deeper layers, which indicates a significant association with the construction background of Lake Longjing.