Well, there's cholera, a disease often transmitted by contaminated water, that often killed 10,000-100,000 people at a time in pandemics 100ish years ago. It is still a huge problem in the developing world (eg 65K deaths last year -- http://www.who.int/gho/epidemic_diseases/cholera/deaths_text...). In the United States, the number of cases per year are typically in the teens, with no deaths typically. (https://www.cnn.com/2013/10/16/health/cholera-fast-facts/ind...)

Typhoid fever is another really nasty disease, often contaminated water transmitted, that still kills hundreds of thousands of people per year (http://www.who.int/immunization/diseases/typhoid/en/). But in countries with clean water and good sanitation the infection rate is very little. As an exmaple: the US over time: https://www.wikidoc.org/images/3/30/Typhoid_stats.gif

I can't say how much this shortened the average lifespan overall, but these are some pretty significant diseases which are largely transmitted by contaminated water (or food), and which are largely eliminated by water and sanitation treatment systems. I'm sure there's some others, these are just the first two that came to mind.

Giardia by comparison is more of a "nuisance", but with treatment methods so cheap (I mean, iodine tablets are on the order .15 a tablet or so) I really don't see a reason to take the risk of that or other stomach-upsetting bugs getting in you.