probably it is not going to work, because in the method small variation of roughness also affects the result and fitting parameters drastically then may be water layer is hard to design on the sample surface.
Ellipsometry is surface sensitive technique works well for a thickness ranging from few nanometer to 2-3 micrometer. It will certainly not work under water. Spreading a thin water layer on substrate will also not serve the purpose as the thickness of water in such an arrangement keep changing and ellipsometry is very sensitive to change in thickness.
However, It is possible to study reaction at the surface of water (air-water interface) using a ellipsometry where change in Delta and Psi (one zone measurement) can be monitored as function of reaction time.
In case, you want to study any reaction that is occurring under water at the surface of silicon (or any other substrate), then take that substrate out of water post reaction and then run ellipsometry. The thickness variation before and post reaction can be precisely monitored this way using ellipsometric angles delta and psi.
in contrast to the previous post, of course ellipsometry is suited for in-situ investigations in acqueous environments, or liquids in general, see, e.g.,
Article Ellipsometric Spectroelectrochemistry: An In Situ Insight in...
Article In situ spectroscopic ellipsometry during electrochemical tr...
https://doi.org/10.1116/1.579520
The trick is, as can be seen in Fig. 1 of the last paper, to immerse the windows from the ellipsometer into the solution, thus the light is always more or less perpendicular to the liquid / window interface, and does therefore not influence the optic signals ...