The soil carries the water of the pond. The sediment or bottom mud of aquaculture pond is an important part of pond ecosystem. The nutrient exchange takes place between the sediment and bottom water, which has a great influence on the water quality in pond. Aquaculture activities will change the properties of the surface sediment, and then affect the growth of farmed animals and yield of the pond system. When the pond sediment is altered to adversely affect farming activities, attempts should be made to remediate the pond sediment. Physical, chemical and biological methods are used in pond sediment remediations. In this chapter sediment and sedimentation in aquaculture ponds, respiration of aquaculture pond sediment, N and P exchange between sediment and overlying water, and remediation of aquaculture pond sediment are introduced.