Hey. I don't really want to comment on the isolation of DNA from drinking water. But don't you think it would be better to isolate the bacteria via something like membrane filtration coupled with selection media? I believe a 0.45 micron filter should do the job.
Then once you have the isolates, you could go for culturing or 16s rRNA based PCR to identify the strains. I believe you can find a lot of papers on it.