Is fertilizing yards good or bad if one has well water? It does get into water systems but what about a well that is at least 100 feet deep? Any thoughts?

this is an amount issue. are you putting bag after bag on the ground.

also how deep is the casing pipe? is it down 10 or 20 feet or more and then driven into the bedrock?

for septic systems, the general numbers are ,,,it takes the waste water to go down through 40 feet of ground till it is purified by the microbes in the soil to be drinkable again.
(depending on soil/sand conditions.)

some wells have casings that have loose soil aroung them leading to contamination going down around the pipe to the well water. a well head should never have ground sloping to it to cause water to sit around the top that can seep down around the casing.if your casing top is below ground ,then make sure mice can not get in there.

and of course the debate rages on on how much fertilizer is too much. on my lawns ,i use a mulching mower that returns all the clipings back to the lawn and it never needs fertiizer.(i don't get the machine to aerate the grass in the spring either.) with a conventional side discharge mower, you cut the grass in a circle so you are always cutting the dis-charged grass on the next cut.(how can you tell i hate raking grass)
with a decently dry lawn(when cutting) and a 6 hp mower engine then you don't have to be cutting every 3 days like some people do.

Properties with deeper wells are generally not affected by surface fertilizer applications. Where fertilizers and pesticides affect groundwater (usually in intensive agricultural areas), an elevation in nitrate content is usually the first indicator. Fertilizer applied consistent with the manufacturer's recommendations is safe. Nitrogen, phosphorus and other nutrients are generally converted by lawns and plant quite rapidly before it can percolate into the sub-surface ground water.