I'm not sure that I can add too much to the conversation, as I've not used Modge Podge. I have, quite a few years ago, used a clear casting resin for water, but it was extremely stinky. At that time, I didn't really plan out the water feature (it was part of a diorama than was intended for photography), and while it look "watery" enough, the smell precluded ever using that particular material again.
...I've read and re-read Dr. Wayne's "tutorial" many times. It's a fantastic look, but not a material I can use in the windowless room and with my wife's sensitivities....
The clear coat on my Durabond water is a water-based, high gloss urethane from Varathane, called Diamond Wood Finish for interior surfaces.
While it does have some odour, I'd liken it to that of latex house paint, and the label claims it to be "virtually odourless". Its advantages are the low odour, the hardness of the dried surface, and the fact that it doesn't alter the colours on which it's applied, and doesn't yellow with age. My layout room is also windowless and my wife's sensitive olfactory nerves were apparently unaffected, as there was no bellowing about "What kinda chemicals are you playing with now?!!!"
It appears white when applied, but clears as it dries. It's dry to the touch in one hour, and can be re-coated after four hours. They recommend three coats, and the exercise of some caution with the surface for about a week, until it's fully cured.
Once cured, the surface is very tough, and my rivers have supported many cameras over the years they've been on the layout, with no evidence of chips or scratches. I wipe the surfaces occasionally when dust accumulates (mostly when I was adding a second level of the layout over the area where most of the water features are located).
I used a 2" brush to apply the three coats, cleaning the brush with water between uses. It's suggested that the user "apply liberally and avoid over-brushing" and the brush marks do disappear on their own. There are intentional brush marks in a couple of my rivers, but they were done in the Durabond, before it set, to suggest motion.
I bought a quart of the clear finish, but the level in the can barely went down at all after covering four areas of "water". I think that this finish should be available in smaller quantities, and suggest that you look for a half-pint. This will be considerably cheaper, and will allow you to determine if the odour is acceptable or not. In fact, you may be able to have the can opened in the store to determine if the odour will be an issue. If your proposed water area is not overly large, and the odour not an issue, that may be all that you require to complete the job.
After the Durabond was applied and the surface more-or-less levelled, I used a drywall knife and a damp sponge to "tease" the surface up into ripples, swells, and waves. This was an on-going process, as the setting time stated on the Durabond packaging is somewhat dependent on the consistency of the mix, and I was worried that it would set rapidly once the process began, with not enough time to create the various effects I wanted. This, fortunately, wasn't the case, but it would have been had I attempted to do all water areas at the same time.
Due to its self levelling properties, the clear finish is not suitable to use for imparting three dimensional detail.
Paint determines the depth of the water and its quality (clean, muddy, polluted, etc.). For shallow, moving water, I used white acrylic paint (Pollyscale), applied with a 1/2" brush, to the "teased-up" rapids, and the small "breakers" on the inlet of Lake Erie.
I don't think that this method is suited to all types of water scenes, but it is a fairly low-cost and easy-to-do option.