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You'll need a lot of leg work, contacts and language skills. Sites like Guidestar could help to some degree, but I feel boots on the ground are a nescessary but not sufficient step toward due diligence. I'd be happy to communicate with you about Guatemala. Each country is different. Our local 'charity' is Agua del Pueblo (www.aguadelpueblo.org). Also check out <www.peopleswater.org>
Best,
Bruce