Contaminated marine sediment is a secondary pollution source in the coastal areas, which can result in increased nutrients concentrations in the overlying water. We analyzed the nutrients release characteristics into overlying water from sediments and the interaction among benthic circulation of nitrogen, phosphorus, iron, and sulfur were investigated in a preset sediment/water column. Profiles of pH, ORP, sulfur, iron, nitrogen, phosphorus pools were determined in the sediment and three different layers of overlying water. Variety types of sulfur in the sediments plays a significant role on nutrients transfer into overlying water. Dissimilatory nitrate reduction and various sulfur species interaction are predominantly embodied by the enhancing effects of sulfide on nitrogen reduction. Contaminant sediment take on high organic matter, which is decomposed by bacteria, as a result promote bacterial sulfate reduction and generate sulfide in the sediment. The sulfur and iron interactions had also influence on phosphorus cycling and released from sediment into overlying water may ensue over the dissolution of ferric iron intercede by iron-reducing bacteria. The nutrients release rate was calculated followed by release rate equation. The results showed that the sediments released large-scale quantity of ammonium nitrogen and phosphate, which are main inner source of overlying water pollution. A mechanical migration of key nutrients such as ammonia and inorganic phosphate was depicted numerically with Fick’s diffusion law, which showed a fair agreement to most of the experimental data.