I deal with this every year as I use our well water to bring the water back up to the right level after the winter. I have a sand filter and it takes 3 days to clear up after shocking the first time. I just use a little liquid floc in the filter and backwash once a day. The backwash water is always dark brown. It just takes time. I have a 10,000 gallon, 21 foot round in ground pool with a large sand filter.