You can play around with this of course but I thought that worked well enough for me. So the reason I chose the shifting that way is because the tile is 16 pixels tall. The animation goes from 1 to 2 to 3 to 1. For the 3rd, I just repeated that process with 5. Then I shifted it down 6 pixels the 6 pixels on the bottom get moved up to the top for the 2nd waterfall tile. It should be on a transparent background. See the rocks brown and ice on the 4th column? You can take a similar approach to this there. For the shadows, it was a simple reducing of brightness for the selected water, but you could do a hue shift too which would get some better results.

Then make it semi-transparent some have it as alpha channel.

If you have a program with layers, put the water tiles on a layer above the floor tile you want to use. Some of the water tiles have shadows on the left side, and a floor tile with water above on the top row of it. I would worry about the shape of the land before you go shading it in, like making sure it tiles. This is good for the water autotiles that have 3 of them in a row. I made the animated ones green and pink so they stand out here. It should go from 1 to 2 to 3 and back to 2 and 1 so it can cycle over. You have 8 auto-tiles which have 3 of them in a row. So if you want waterfalls, use them in the correct spots. Instead of animating like a waterfall does, it shows the first frame, then shows the next 2 water frames to the right of it. For example, I put a waterfall tile block over the bottom left side. This site will stop updating, but the updates will continue in the new site.

How to make rpg maker mv tilesets