Job One is to properly identify the plant, as ThePondDragon suggests.
Chara, exposed to dry air, will die. It will turn white and crumbles into dust. But, that plant reproduces sexually, believe it or not. There are male plants as well as females. During the season, zygotes are formed and drop to the bottom of the pond. They sprout the following spring, when water temperatures are right, and new plants start. So, even if you lower the water to kill existing plants, you don't eradicate it. When water covers the bed where tiny "seeds" are, they'll grow.
The follow up to that is this: Chara isn't a 'bad' plant. It will carpet the pond floor where sunlight penetrates, holds loose soils in place and prevents other, often more invasive, plants from growing. I personally prefer Chara to some of the others. It becomes a "problem" when we can see it, and when the water level drops as to present the plant near the surface.
