Firm reason number 1: it may create a legal right in the two properties which don't have the quality water systems, and put the 'good' property under an easement, which is a legal liability. Your friend's gut is telling him the right thing. To sort out the property rights, the neighbors would each need to hire a lawyer (one lawyer should not represent the three, as there are conflicts of interest among the parties) to haggle out the privileges and liabilities of each owner as to the water and wells. Joining the wells involves rights and obligatons in real estate that would pass to each successive owner and encumber each property. There should be a recorded instrument which alerts potential buyers of the easement, and existing title policies might be affected. The property values of all three parcels may be affected, and there might should be some compensation due one or more parcel owners as a result.

Firm reason number 2: it may be that there are costs to "join" the wells and pumps and there will be ongoing maintenance costs, and the parties need a written agreement to take into account who is obligated for what costs or compensations for what benefits. Each should have his or her own lawyer, as there are conflicts of interest. The agreement should provide whether each person funds his or her share in advance, what happens if someone fails to fund a share; or whether costs will be paid as the project goes forward, again with provisions for failure by some party. There are ongoing costs, which should be provided for in the agreement, along with provisions for failures on the parts of the parties.

Your friend should talk to a lawyer who specializes in real estate law, especially in easements, and who knows about local water rights. Different regions in the US have different laws on water rights, depending on historical scarcity.