A seed becomes a tree, which falls and decomposes, becoming the soil and nutrients that created it. All of nature has stages and cycles of life. This includes the pond. A pond has an ecological cycle and food chain of its own.
Plants grow from nutrients in both the water and sediment.
For fish to grow, they eat algae and plants. When the life of a fish or a plant is over, it falls to the bottom of a pond and decomposes into organic sediment along with other fish and plants. But there are other contributors to this layer of sediment at the bottom of a pond. Any deciduous trees or plants surrounding the pond shed debris into the water. This material is also left to decompose on the bottom.