I found this near the top of a search for Bitcoin accepting charities, but it only has 8 or 9 charities on its home page. I don't know if it's reputable and I agree with other posters that some big charities spend all the donations on inflated wages. It's best to find out how much of the donations goes to the people who need it before donating.
https://bithope.org/campaignsChecking a charity is not easy. Eternalgloom said you can use his charitynavigator.org link to check,
... you always have to look up a charity on
http://www.charitynavigator.org/You'll see how much of the funding actually gets spent on the cause in question and how much goes into 'overhead'.
However when I tried checking the thewaterproject.org link posted by Invulner I didn't find it rated by charitynavigator.org.