How long will it take to get water mold out of a pool that uses baquacil?

It should only take about a day or so. The best thing to do is add the Water Clarifier to the skimmer with the filter running, add Flocculant as a filter aide and let run for 8-12 hrs, vaccum to waste, and chemically clean the filter. It is very important to chemically clean the filter because while vaccuming to waste the water mold will trap itself in the filter and can filter back into the pool and start to form again. It is best to chemically clean the filter to kill off any water mold that may be left over.