Over the past several decades, there have been a number of national and international meetings on waterborne diseases. Conclusions from these meetings often seem remarkably similar and suggest little progress in the field of water and health. This is both a true and a false premise, as our ability to use molecular tools to describe microbial communities has advanced to the level at which whole genome sequencing is now a routine practice and can even be deployed in the field. This article seeks to illustrate both these advances and their limitations, especially for use in low-resourced settings. What remains clear is that for most of the world, basic hygiene and sanitation measures can do more for human health than any of our current advances in molecular biology. That is not to say that these advances are not remarkable and that they can undoubtedly revolutionize risk-based testing and surveillance. Although there are many factors that contribute to increased risks from waterborne diseases, climate change above all else is creating challenges that we are ill-prepared to meet. The biggest barrier to control of these diseases is not limitations in technology but has been and continues to be the lack of political will and economic incentives.