I can wholly empathize and understand your passion for combining your two hobbies. Adding "live" water is a huge project. I have been in the hobby for 50 years, I've tried it on a couple of occasions. One time it didn't work and was a disaster, the second time was a bit more of a success. Even then, it was not without its problems.
My critiques, though negative, are only to prevent you from becoming disenchanted. The foreseeable problems far outweigh the benefits and hopeful outcome. The reality is that water and trains, and electicity, are not the best of friends.
My layout has been 12 years in its evolution. It is large by most standards. We are even going to build a separate building for it. It, quite literally, takes up the whole basement, save 12x20 area for the fish room.
You will notice that I said evolution. I am constantly build new modules, rebuilding and remodeling others. Tweaking, if you will. What started out as a 10x16 L-shaped layout in a spare bedroom, now covers over 1200 square feet, and takes up even more room. The 1200 SF is just tables, though I rarely set up all of the module, nor would I even if I had the space.
Your plan, and dream, is truly ambitious. Not for a beginner or even an intermediate modeler. It may take years to accomplish the end product. Research alone may take the better part of a year, or more. And, surely, the cost will be in the thousands. And add in the "human" factors of lack of patience and loss of interest, you may never realize the dream. The process is going to be a slow one. Slower than any of your turtles. You will see spurts of progress, and then see, what may seem like, digression. Been there all too many times. And, too, sometimes life just gets in the way. You will need the patience of Job to see this to the end. And maybe the lifespan of Methuselah.
Planning and engineering alone are going to be colossal undertakings. Water runs downhill, so you must make sure you have enough " fall" toward the "drain. The "plumbing' will have to be designed. The riverbeds will have to be absolutely water tight. The splash from any water fall will have to be contained. In these areas, you will probably have to use a resin(fiberglass) of some sort. Seams and joints in these areas must be absolutely waterproof. And to make the system more "hands-off" I would suggest a "water level top-off" system with a supply line to keep the water level in your sump adequate, much like in some aquarium set ups. Nothing worse than to have to do added maintenance.
That is another subject to broach. Maintenance. Track cleaning,, and added water changes for the herps. I think that alone would be over whelming when added together. Slop a bit of water on the layout and things could be ruined. Accidents DO happen. And according to Mr. Murphy, they occur at the worst possible time and do the worst possible damage.
I don't mean to discourage you, but the reality is there. It's staring you down. And it WILL come to fruition. Even a design fitted to a worst case scenario can go awry. Take it from one who's been there.