In order to study the application and the effect of ecological dredging and silt disposal in deep-water reservoirs, the ecological dredging and regulation engineering of Tongjiqiao reservoir was taken as an example. The influence of dredging on the pollutant diffusion in bottom sediment of the reservoir was analyzed through tracking and monitoring the water quality near the cutter suction dredger and reservoir intake. The moisture content of the dry soil after plate and frame filtration treatment and the residual water index was also tested and analyzed. The result shows that the ecological dredging only causes sediment disturbance within 20 meters from the ecological cutter with a short duration, which has no obvious influence on the water quality near the reservoir intake. The moisture content of the silt obtained by dredging can be reduced to 40%-60% after the rapid dehydration treatment, which meets the requirement of sediment transport and resource utilization. The residual water also meets the standard emission requirements during this process.