A method for remediating a body of water includes sequestering a sector of water within the body of water. A communications channel is established between the water sector and a supply site. The water sector is at least partially remediated using the channel to alter a composition and/or a state of the water in the water sector. The channel may be used to add a chemical or nutrient; to provide air or water for mixing the column contents; to convey an electrical signal to an element such as a valve, sensor, or pump in the water sector; to withdraw samples and/or components from the water sector; or to obtain information therefrom via electrical signals. Following the remediation, the remediated water is exchanged with water to be treated from the body of water. In this way, the body of water is remediated over time.