Heavily polluted sediment is becoming an important part of water pollution, and this situation is particularly acute in developing countries. Sediment has gradually changed from being the pollution adsorbent to the release source and has influenced the water environment and public health. In this study, we evaluated the pollutant distribution in sediment in a heavily polluted river and agitated the sediment in a heavily polluted river to re-suspend it and re-release pollutants. We found that the levels of chemical oxygen demand (COD), NH4+-N, total nitrogen (TN), and total phosphorus (TP) in overlying water were significantly increased 60 min after agitation. The distribution of the pollutants in the sediment present high concentrations of pollutants congregated on top of the sediment after re-settling, and their distribution decreased with depth. Before agitation, the pollutants were randomly distributed throughout the sediment. Secondly, deep sediment aeration equipment (a micro-porous air diffuser) was installed during the process of sedimentation to study the remediation of the sediment by continuous aeration. The results revealed that deep sediment aeration after re-suspension significantly promoted the degradation of the pollutants both in overlying water and sediment, which also reduced the thickness of the sediment from 0.9 m to 0.6 m. Therefore, sediment aeration after suspension was efficient, and is a promising method for sediment remediation applications.