It's tricky. I like how aamatniekss handled it in Era of Fantasy, by giving shallow water the texture of the ground below it, and underwater chasm tiles that transition to water deep enough that you can't see the ground anymore. (I took a similar approach in my own set, Land and Sea, which is more gameboy-oriented.) But obviously this means you'll have to treat every single shallow water ground differently and think carefully about how you palette them; this isn't a one-size-fits-all solution.
Viewing post in How to do water depth tile transitions?
So, upon further investigation, I think ive been shifting my values in the wrong direction.
All of the colors I have are super saturated, which can be an style all its own, but its not working how I want. Ill have to adjust my palette and see if I get a better result.
Another thing Ive seen is the devlog for a game called Dauphin on YouTube, and how he approaches it is opacity. As long as the texture underneath is interesting but not distracting, that is another option