Help! My pool is covered with algae! What do I do? Test your pool water. You will need to shock the pool and possibly add an algaecide as well. Balance all chemicals to proper ranges. Vacuum off the algae from the floor and walls. Brush off any algae that is in the corners, seams and step areas. Keep your filter running, and backwash DE filters frequently until the water is clear and all the algae gone. Sand filters may clear water better if they are a little dirty. Cartridge filter will have to be cleaned several times a day until the water is clear.