A system to control nutrients, suspended algae, and filamentous algae in lakes, ponds, and estuaries includes a structure for containing macrophytic vegetation. One embodiment segregates a column of water within a body of water desired for remediation and shields the water column from sunlight sufficiently to kill phytoplankton therein, the lysis thereof releasing nutrients. The released nutrients are sequestered, and remediated water is replaced in the water column with water from the body of water. Floating or submerged macrophytes can be introduced in combination with shading and induced water movement to optimize nutrient uptake by the macrophytes. Water column shading may also be achieved by the macrophytes themselves, or by other means. The macrophytes can include floating aquatic plants, such as water hyacinths, submerged aquatic plants, and terrestrial or aquatic plants caused to float artificially. The invention also deals with toxic algae in a safe and sequestered way.