Typically, anything that becomes "a permanent part of" the structure is added to the cost basis of that structure. If the property is being used in a business (such as a rental property) then it gets depreciated over time from the date it was placed "in service" in that business.
For some non-real estate assets that cost less than $2,500, you can chose to either add it to the cost basis of the property, or outright expense it under the de-minimum safe harbor provisions. Now hot water heaters are their own beast. One would typically think to classify it as an appliance and depreciate over 5 years. However, a water heater becomes "a physical part of" the plumbing system, which is already a physical part of the structure. Therefore, it would be classified as residential rental real estate (assuming this is a rental) and depreciated over 27.5 years.
If the well pump is just an irrigation pump, that's a simple repair expense. However, if the well is the primary water source for the house I'd treat it the same as the water heater, since it does become "a physical part of" the plumbing system. If the new pump was less than $2,500 (I'm confident it was) then no problem expensing it really.
Now, depreciating a water heater that cost on average $800 (and that includes installation) isn't going to amount to anything worthwhile each year, depreciated over 27.5 years. For me, I'd classify it as a repair expense and just deduct the $800 and be done with it.
