Upfront costs per unit
Part of this will be the cost of making a transmitter/receiver pair vs the cost of operating it. If a tranceiver costs $1/square inch to make, then every city water system can abandon it's plumbing infra-structure. Every house has a receiver.
At a somewhat larger cost, cities like Phoenix, AZ that are currently pulling water from 9000 feet below the surface, and dropping the water table by 50 feet per year have a new lease on life.
If a 24" unit costs a billion dollars, then only large corporations and governments can use it.
(One thread that can run through your novel is the impact as the price per unit comes down.)
Your story will work better if there is a cost. Not financial, but in the form of constraints on its use. Is energy conserved? E.g. if you move water from Los Angeles to Denver, do you have to add energy the equivalent of lifting it up to Denver?
Does the water come out at Denver moving at the velocity of LA? This would allow you to weaponize it. E.g. there is a ~1600mph difference in velocity between Miami and Saigon. This becomes a way to tap energy from the system even if it does conserve energy. You're slowing down the Earth.
Can the system be tuned to handle any pure substance is liquid or gas form? If so, you just replaced all pipelines for everything. Keep filling up the fuel tank of a rocket while it lifts off? Even if you have to pay the energy cost for both the gravitational potential energy and the velocity difference of the rocket, it would still be far cheaper than conventional rockets.
If it's really cheap you can use it as a climate weapon. Make a gate a mile across and put the intake in an antarctic current with the output in the Aegean Sea and ruin the Italian wine crop and air condition Greece. Raise the temperature of the Humbolt current and destroy the anchovy fishery. Drop enough fresh warm water south of Greenland and turn off the gulf stream.
Flood low-lying parts of the Sahara. Evaporation and rainfall makes the areas around the new lakes fertile. This changes the balance of power. It also means the present inhabitants need to learn a new life style.
Build one the size of a 2 inch pipe, and give them away to every poor village.
If tuned to water, what happens if you try to pass an object containing water. E.g. Would a water bottle come out the other side of a transmitter empty, with the contents sent to Lower Goatsbreath, Manitoba? Does this become an instant way to dry food? Does it kill if the transmitter field is aimed at a person, drying them to mummy dust in a split second? Step out of the house, zot the house and kill all the termites. As well as the house plants and the goldfish.
This of course requires that the magic be outside the device.
If the units are small and light enough you could cover parts of the Sahara with black plastic. The air underneath gets hot. You can now replace every forced air furnace in the world. Or hot air balloons can stay up indefinitely. (Ok, you need two deserts on opposite sides of the world. Finally: a use for central Australia.)
Tune it to whatever metal. Put the device in the gulf stream the water passes through, the metal goes to the receiver. Tune to CO2, put the receiver 3000 feet underground in a salt water formation, and you take the CO2 out of the ocean. (Ocean holds a LOT more CO2 than the air does.)
If it can be tuned to any one molecule, but others pass through entirely without force, then it can remove that substance from a living person. If you are exposed to Cesium 137 from Fukushima, walk through the screen, and all Cesium 137 (or all cesium?) is removed from you. Run all the top soil through it, and people can come back to the area around Chernobyl.
Only simple molecules -- probably initially. But suppose later you can tune it to a specific protein: One pass through and you get rid of the accumulated protein that may cause Alzheimers. Or the poison in amanita mushrooms. Tune it to plaque in your arteries, and rejuvenate your circulation system. (It's more complicated than this...) Or tune it to a protein found only in Caucasians, and Uganda has the ultimate racial cleansing tool.
Clean up toxic waste sites? Tune to a spectrum of hydrocarbons, and clean up oil spills. Pull asphalt out of highways, turning them back into gravel roads. Separate rebar from concrete. Recycling becomes a series of towers with a chain of tranmitters. The first few pull out heavy metals and volatiles in plastic. Then common metals such as iron. If it can be beamed you could take all the iron out of a skyscraper or a dam. Take out all the aluminum of a plane in flight.
Can it be tuned to individual isotopes? The biggest problem in building an atomic bomb is separating the right isotopes. Disposal of radio waste becomes easier. Separating isotopes for specific medical use becomes easy.
Can you take all the water out of a parcel of air on a scale large enough to create rain shadows? Or put water vapour into a parcel of air for snow making at a ski hill?
Solar system development
Hauling fuel is the biggest cost of moving stuff around the solar system. If it works with ice, you could transport ice from Saturn's rings to the surface of Mars, making that place a lot wetter. Siphon off 99% of Venus's atmosphere and store it on one of Jupiter's moons. Float one tuned to helium in Jupiter's upper atmosphere, and we'd never run out of party balloons. Tune it to Methane and crank up Mar's greenhouse effect. Tune it to CO2, and adjust the thermostat on Earth. If we can tune to isotopes, then separating hydrogen from deuterium from tritium becomes trivial.