I always find it interesting when two completely different words are spelled the same. Well, like a water supply, has nothing in common with well as in good.
Looking at their histories, the good well is from the Old English wel and was similar throughout all the Germanic languages. In some translations, it still is. In Swedish they have val, in Dutch wel, and in Icelandic vel. It can be traced as far back as the Proto Indo Europeanwel/wol, which means pleasing and is also the origin word for will.
The hole in the ground well is related to another definition of well (how one would well up with tears). This well comes from the Old English wiellan and is related to their word for boil, weallan, probably because of the bubbling water. Its Proto Indo European word is also wel, however in this case the definition is "turn or roll." I guess they may have had words with two meanings as well (we can only assume since what we know about the language is guesswork).
Unlike the previous definition, this word is fairly unique to English. I would have to say this is because it was more heavily influence by the speech of Angles (as in the Anglos, the Germanic tribe that spread across Europe; their name is where the word England comes from) than other languages of Germanic descent. Basically, Swedish, German and the rest found a word they liked better. We did not.