I'm curious about the algae. I have never had algae "sit on the bottom". My only experience with algae has been when it is suspended in water giving the whole pool a green tint. Occasionally, you can see it in tiny crevices around the edges of the pool that get poor circulation but I have never seen it on the bottom. Do you have other debris sitting on the bottom that has turned green from algae?

Nevetheless, the answer is, as stated above, vacuum out everything you can first. You will still need to chlorinate heavily......you will still have suspended algae in your water.