Taking the Beitang and Dagu Sewage Discharge Channels in Tianjin, China, as study objects, concentrations of heavy metals and organic matter are determined in upper layer, middle layer and lower layer sediment samples. Geo-accumulation index method and correlation analysis are taken to study the distribution and pollution level of metals between layers in the two channels contrastively. The results show that the concentrations of heavy metals greatly vary among each layer sediment, proved by the fact that the coefficients of variation of heavy metals concentrations differ in each layer. The main pollutants are all Cd, Zn and Cu, and Cd is the most heavily polluted element. The correlation of heavy metals and organic matter concentrations shows a reinforcement trend from upper layer to lower layer. Besides, the difference of pollution level between layers is larger in Beitang Channel than that in Dagu Channel, and the correlation of each pollutant in each layer sediment in Beitang Channel is more significant than that in Dagu Channel.