The exact state of a system is defined by a set of parameters. In thermodynamics, we can prove the thermodynamic state of a closed system with the same mass of a pure compound (your glass of water) is defined by only two of the three parameters (T, p, and V). Unless one process changes the pure water to something else chemically while the other does not, the two systems of pure water at the same (T, p, V, and m) will be indistinguishable. This is especially true to a "casual observer".
You might ask whether one process (microwaves) can leave a different distinguishing signature about itself on the pure water that another (conventional oven) does not. Focusing only on microwaves, the fundamental interaction is generally to increase the rotational energy of molecules. Focusing on convectional ovens, the fundamental interaction is generally to increase the overall energy of the modes of translation, rotation, and vibration. In this case, translation is easiest to excite, followed by rotation, then vibration.
You might expect then to find that water heated by microwaves is distinguishable from water heated by a conventional oven using a tool that can tell which modes are more populated. In a process that uses microwaves, the rotational modes of the pure water should be more highly populated, or so you might suspect.
However, excitation of the rotational modes cause the molecule to bump into other neighboring molecules and transfer the energy. The energy transfer happens to create a thermal equilibrium throughout the water.
So, while the water in the microwave heats up ...
- the water molecules are excited to higher rotational energies
- the excited water molecules transfer the energy by collision to translation and vibrational modes of their neighbors
- since translation is easier to excite than vibration, the rotational energy is transferred to vibrational energy
In the meantime, in the conventional oven, all modes get excited (translation first, then rotation, then vibration).
At the end, pure liquid water at a given temperature, pressure, volume, and mass is the same regardless of how you brought it to that state. The modes (translation, rotation, and vibration) are all normalized to the same population statistics. That indeed is the definition of an equilibrium temperature state for the pure water itself.
Quite a different picture will arise when you take an individual water molecule in a gas phase. You can excite that molecule thermally by having it bounce off of a hotter surface. The water molecule will move faster or rotate in the next highest state or vibrate in the next highest state. You can do this using only an infinitesimal amount of heat, but that will only cause translational excitation. You can excite an individual gas phase water molecule rotationally by hitting it with the right quantum level energy (frequency) of microwave radiation (determined as $\Delta E_{rot} = h\nu$). It can remain in that state until the energy transfers internally to other modes. This is internal relaxation of the excited state. Otherwise, the molecule will loose the excited energy when it collides with a system or molecule, especially one at a lower energy state. You can excite an individual gas phase water molecule vibrationally by hitting it with the right quantum level energy (frequency) of infrared radiation. Finally, you can excite an individual gas phase water molecule electronically by hitting it with the right quantum level energy (frequency) of ultra-violet radiation. In each case, you can usually detect the internal decay (relaxation) of the excited state (rotational, vibrational, or electronic) by looking for emission of radiation. By example, a fluorescent molecule is one that has been excited electronically and is relaxing by emitting visible radiation.
Excited states are not ground states. They are not the thermodynamic system of pure liquid water after it is heated. To capture the excited state of the water molecules, you have to isolate them. The minute an excited state molecule collides with another molecule, energy is transferred.