We've dealt with similar ...
Published by Betsy VandeBeld, www.betsyhr.com - Consultant
We've dealt with similar issues (underground cisterns and outdoor cisterns in Canada, and rooftop cisterns in Brazil). Although all sediment/debris has to be removed manually, it is possible to steam clean if you have the right equipment. Other than than, a chemical soaking (bleach/chlorine) is the only alternative we have found that can guarantee water safety for your clients.
Best of luck to you!
Betsy at www.ptlevel.com