Basically the power of "Writing" overrides pretty much anything we know about physics.
Here's an excerpt from the Book of Atrus, from when Atrus first learned that Catherine (or anyone) was capable of writing ages.
"The writing ... well, as I said, the writings wonderful. It's poetic. But in practical terms . .. it's riddled with contradictions, I'm afraid. It breaks almost every single law of D'ni writing.It has no structure, no architecture. And some of these symbols . . . I've never seen them before. I'm not even sure they mean anything. Where did you learn them? Gehn never taught these to me."
"For such a place to exist..." Atrus sighed, then, closing the book, handed it back to her. "I'm afraid it wouldn't work, but it does paint wonderful pictures in my mind."
She smoothed her fingers over the pale lemon cover. The green and light blue flecks in it hadalways reminded her of grass and water, the predominant yellow of the sun. Fecund, it was, like the world surrounding her, but inside..."
That's good," she said. "It must be like a dream."
He stared at her, not understanding.
"When I go there ..."
He shook his head. "But you can't..."
"It was just like my dreams," she said, turning to face him again.
"No," he said forcefully, taking the book back from her. "It simply wouldn't work. Writing isn't like that. Its a science. A precisely structured equation of words."
She leaned across him, then opened the book, pointing to the descriptive image on the right-handpage. It was dark, so intensely dark that he had thought it blank. But there was something there.
He looked to her.
"I want you to see it."
"It's..." he said, softer now, the word almost a whisper. Yet even as he said it, she leanedacross him and placed his hand upon the image, smiling at him, her smile dissolving in the air ashe linked.
Atrus stepped out of the air into a huge, conical bowl of darkness. And in the middle of thatbowl, at the precise center of the massive, mile-wide hole that pierced it, a powerful column ofwater-as broad as a river-thundered straight up into the darkness until it was lost from sight, agreat spike of brilliant, crystalline light glowing like a fierce flame at its center where itemerged from the glowing depths. Atrus stared, dumbstruck.
Things behave the way they do in ages because they were written to behave that way. In the games, we encounter ages that behave according to what we expect, because all the ages in Myst, for example were written by Atrus, who is very much a man of science. Riven was written by Gehn, who was known for his flawed writing, so the water's behavior could be due to said flaws, or knowing Gehn's personality, it's sole purpose for existing was simply so he could make those neat water tunnels.