OK. I hadn't understood that. I thought you were saying there was still green algae.

Brown algae is dead. And yes, when the calcium 'sand' is present, the algae will remain brown inside those nodules till it's bleached out by sun and/or chlorine.

There probably IS some live algae inside some of the bits, but if everything you can see is brown, then you can move own. So do this:

1. Use muriatic acid to lower your pH to just below 7.0. That is, add acid till you reach 7.0, and the add a bit more. Read http://pool9.net/muriatic/

2. Dose with chlorine nightly, to maintain chlorine levels above 5 in the AM.

3. Brush the scale after adding chlorine, if you can. Don't brush hard, just enough to knock loose what's already coming loose.

4. Complete the pool chart: http://pool9.net/pf-chart/ so we can see what sort of pool you have.

5. Increase aeration by adjusting the return eyeballs to 'riffle' the surface.