I know this is not what you've asked (I will get to that too), but I figured I would take the opportunity to state that the owner of the well cannot send you an invoice for the water unless you agreed to a price and entered into a binding agreement. They cannot just decide their water is worth X and then tell you that the amount is due. Just as you cannot send them a bill, in the same amount, for the use and maintenance of the pump.
While the well may be located on one parcel of land, with the pump on the other, chances are, the properties were linked at one point and that is why there is a separation of the two (unless you bought it as one and divided it yourselves). This should have been dealt with on the deed, with easements appurtenant to the neighboring land regarding water rights. A contractual agreement could have been attached by reference that dictated the land with the well would maintain the well, while the landowner with the pump would maintain the equipment (or whatever you both agreed to regarding upkeep and the like).
Depending on the state you live in, the property itself may not even "own" the well. For instance, in Colorado, water rights typically come by way of 100 or 200 year leases, as the native american tribes of the area "own" the water rights. Other states have laws that declare that nobody owns the water table, hence land is only owned as far down as the water table and then it is owned by the county, or state, with easements running with the deed. Other states, (I'm wondering if this is your issue) the water runs in veins and does belong only to the property that it is below – as there is no water table, so to speak. Regardless, I would talk to your title insurance policy company and ask why this easement was not addressed in the deed.
I'm assuming that you did not divide the land yourselves, post purchase, and the land with the pump cannot access the water table without going onto the land of the other. Otherwise, it would be very easily solved by drilling your own well (and much cheaper), whereby you already own all of the equipment to run the water to the dwelling. You just divert your equipment to the running of your own well. It's only a few dollars a foot to drill a well, unless you live in the Granite State!
Likewise, you should check with your land assessor's office, or registry of deeds, and see how the title ran back regarding water. Again, depending on jurisdiction, you may be able to drill down and over. You cannot divert, but you can access, in most jurisdictions. I say to contact your title insurance company, because the water issue should have been dealt with at title examination, and further, if your land is inaccessible to any water, it would not be sub-dividable for dwelling purposes under almost any zoning law I have ever heard of. A property that is land locked, or utility inaccessible, cannot be zoned for dwellings, without irrevocable easements or rights of ways, respectively. Just because you purchased near family doesn't have anything to do with any of this analysis. They could be anyone, or you could end up at odds, the water cannot be relationship dependent and you cannot be held hostage over natural resources. If so, I would sue the title insurance policy for a refund of the purchase price or the negotiation of the purchase price of an easement to the well/water table, assuming you have none under your land and have no existing right to it.
If you just happen to have the pump, and they have the well, you own the pump and they own the well. Simple as that. You do not have to allow the pump to be used for their well. Assuming you can drill your own well, but may not want to, you can just rent them the use of the pump at the same rate they are charging you for the water. You can agree to split the cost of maintenance of each, since you've invested in the upgrade of the pump.