It was a good idea, but a pendulum in water will behave differently than a pendulum in air. Looking in section $2$ of your link, Reynolds number is given by
$$Re = \frac{\rho L |v|}{\mu}$$
The derivation that follows is valid for sufficiently low Re. But $\rho_{water} \approx 1000 \space \rho_{air}$.
There are two sources of drag. One is friction. Not just from an object passing through a fluid, but the object makes nearby fluid move faster than far away fluid. Parts of the fluid moving at different speeds exert friction forces on each other. This is called viscosity.
The other is the the object must push fluid out of the way, and fluid must flow in to fill the space behind the object. The fluid is accelerated up to a speed and then back to a stop. The moving fluid has kinetic energy which comes from the kinetic energy of the object. The object must exert a force on the fluid to accelerate it. These are called inertial forces.
The definition of Re is the ratio of inertial forces to viscous forces. The formula is an approximation. In most objects, one force is much larger than the other. You usually can ignore the smaller force. An approximate is all you need to decide which one is way bigger. Reynolds number is a useful rule of thumb, more than anything exact.
Things that make inertial forces big (and therefore Re big) are things that make $1/2 m v^2$ big. For example, a dense fluid, a high speed, and a large object (which pushes a lot of fluid around). Things that make viscous forces big (Re small) are a viscous fluid.
So your pendulum in water is dominated by inertial forces, where the experiment is expecting viscous forces to be the big thing.
You can modify your experiment to run in air, but have bigger viscous forces.
Try using yarn for the string, which has a lot of little hairs that create more friction without adding much mass.
Try keeping the speed low by using a smaller amplitude.
Try using a light mass on your pendulum.
This last one is a little misleading. This doesn't change the inertial forces. That comes from the mass of the moving fluid. The shape of the object, not the mass of the object, determines how much air is pushed around.
But given forces that slow the pendulum, you have $F = ma$. A small mass means a larger acceleration. The forces slow a light mass more effectively than a large mass. That will make damping easier to measure. Think of using a balloon for your mass vs a water balloon.