What is the relationship between Cholera and water supplies?
As noted in wikipedia, “Transmission [of cholera] is primarily by the fecal contamination of food and water caused by poor sanitation.” People drinking contaminated water is an important cause of spread of cholera.
I just don't know how scientists can predict Cholera through water supplies!
Neither of the sentences you quoted are worded as well as they should be. While it is clear that “There was no way to predict how far it would spread through water supplies” is not about “predicting Cholera through water supplies”, it is not clear precisely what meaning was intended. The sentence can be interpreted several ways with several different meanings:
It could not be predicted how far cholera bacteria would travel in the water supplies –or– It was infeasible to predict how far cholera bacteria (which were in water supplies) would spread –or– It was not known that cholera bacteria would spread as far as they did in the water supplies of Haiti.
Details aside, the sentence claims it was not predictable how far cholera would spread.
I guess “help was in short supply” means we provided little help to the areas that needed help most. However, I still don't understand the last sentence.
You've correctly interpreted the “help was in short supply” part of the sentence. The earlier part, “And not knowing where help was needed always ensured that...” perhaps exaggerates for effect. It expresses a logical fallacy by misuse of always (“At all times”) and ensure (“To make sure or certain of something”). Certainly, lack of knowledge of needs typically leads to some misallocation of resources, but does not actually do anything to make sure that areas in need of extra resources never get them.