Vtyjkyuk

This very much exists in the real world, on a colossal mind boggling scale. It is not brand new tech but it is still super useful and still amazing on many levels. Here is a fine example:

https://cleantechnica.com/2018/07/26/city-of-los-angeles-wants-to-turn-hoover-dam-into-worlds-largest-pumped-energy-storage-facility/

The Hoover Dam, 8th Wonder of the World. The molecules involved are those of concrete and steel and they can indeed be switched into and out of place with giant mechanisms. And as requested, the giant barrier that is the dam does very much convert water molecules into energy. The cool thing - you extract energy from the water and then still have the water molecules when you are done!

What you are referring to is not science fiction, it is science fact. Biological science in particular. An example is the fat (lipid) molecule.

Nonpolar molecules that repel the water molecules are said to be
hydrophobic; molecules forming ionic or a hydrogen bond with the water
molecule are said to be hydrophilic. This property of water was
important for the evolution of life. Hydrophobic interaction plays the
most critical roles in the formation of the lipid bilayer of the cell
membrane and the folding of proteins and nucleic acids; therefore,
hydrophobic interaction is the foundation for the existence of life.

https://www.nnin.org/education-training/k-12-teachers/nanotechnology-curriculum-materials/water-race-hydrophobic-0

You might also want to research soap.

Washing up liquid is a kind of soap. Normally, oil and water don't
mix, so they separate into two different layers. Soap breaks up the
oil into smaller drops, which can mix with the water. It works because
soap is made up of molecules with two very different ends. One end of
soap molecules love water - they are hydrophilic. The other end of
soap molecues hate water - they are hydrophobic

from http://www.planet-science.com/categories/under-11s/chemistry-chaos/2011/06/soap---how-does-it-get-things-clean.aspx

However, it is not yet scaled up to the size you want. But doing so is just a matter of economics and the availability of capital to do so. It would 'just' take a lot of engineering and the blending of engineering with biology.

But unfortunately, the bottom line is that no matter how hydrophobic the molecule, you are faced with the mechanical problem of holding back the pressure from the water. That is, it is not difficult to make a huge barrier of hydrophobic molecules, but it would just be swept away by the force of the water. How do you reinforce and anchor the membrane? Somehow, you would need a huge counter-pressure. Say, a very highly pressurized bubble, perhaps?

But then, it is not the hydrophobic qualities that are holding back the water, it is the mechanical properties of the structure that contains the hydrophobic molecules.

Based on the question as it is now, a sort of solid energy barrier to block water, you would need a cold plasma shaped by magnetic fields to act like a barrier.

Plasma is just ionized gas, such as evaporating wax as it's burning at the top of a candle. It's quite easy to control the flow of plasmas within electromagnetic fields.

To ionize something, either add electrons or strip away electrons. A high voltage antenna such as a tesla coil can ionize air quite easily, making spectacular arcs of lightning fly out. The process goes on in fluorescent light bulbs, neon signs, all TVs except for the LED based ones, etc., and as I said earlier, from many chemical reactions that cause things to burn.

What is beyond the realm of physics, though, is a way to keep a gas ionized while it's in contact with water. Since non-purified water is an excellent conductor, as soon as a plasma touches it, the plasma is grounded out, bringing the number of electrons back to a neutral state.

Since your gas is in a neutral state, it's not a plasma any more, so can't be directed by magnetic fields.

This is where you'd use some handwavium: a gas that stays ionized even when in contact with an excellent conductor.

Alternatively, you could keep on bombarding the seas with newly ionized plasmas accelerated towards the water by vast arrays of plasma "guns" (which would resemble a gun in much the way a wide nozzle power washer resembles a gun; it's not a single kinetic round travelling in a ballistic arc, it's a steady stream of particles spraying out and expanding out in the same general direction) but then it's the wind pushing the water back, not any sort of "energy barrier." You might as well just get tons of fans to blow the water; as it would be far more efficient and just as hilarious.

If you want to avoid handwavium, though, just set up inflatable dams like they have protecting some inland lakes from storm surges in the Netherlands.

To answer the question, this is a short and sweet one:

What you are asking for doesn't exist using any known science - therefore there is no known plausible or hypothetically possible way to do it.

... There may well be ways to solve the problem that are physically possible though if you are able to ask another question defining your requirements or you can just do what other similar sci-fi does and hand-wave the force fields into existence by assuming some scientific breakthrough. If you do that you can give them whatever properties you need.

Is it hypothetically possible to create a giant levee which can be switched on and off that acts as a “water-molecule negating” shield?

There are at least two spillways in Louisiana on the Mississippi River.

https://en.wikipedia.org/wiki/Bonnet_Carr%C3%A9_Spillway

The Bonnet Carré Spillway /ˈbɒniː ˈkɛriː/ is a flood control operation in the Lower Mississippi Valley. Located in St. Charles Parish, Louisiana – about 12 miles (19 km) west of New Orleans – it allows floodwaters from the Mississippi River to flow into Lake Pontchartrain and thence into the Gulf of Mexico. The construction of the Spillway was completed in 1931.

Basically, it's a set of gates in the levee. They remain closed except during times of unusually high water during spring floods.

Water is actually effected both by electric charges and by magnetic fields, but either requires such a strong field that you would basically be making a levee out of electromagnets or modified telsa coils and still not blocking the water completely.

https://www.quora.com/Why-doesnt-a-magnet-attract-water-the-way-a-static-electricity-charged-balloon-does

Standing Waves

This is where a mechanical device creates vibrations in the water such that a wave is formed, but it interacts with other water movement so as to create a wavetop that doesn't move.

For instance, canals could have "standing wave locks", where instead of gates the standing waves are manipulated to float the boat up. If the locks we built long, the boat wouldn't even have to slow down.

In flood control, the standing waves would simply keep the water out and up at the top of the wave, which never makes any headway toward shore.

Of course if the power fails, instant tsunami...