You’re not alone — depth bands + shoreline edges are where tilesets get noisy fast.
Palette tip from the thread is solid (desaturate/darken deeper bands). For the edge between land and water, a dedicated transition/corridor set usually reads cleaner than forcing one noisy texture to do everything.
If you want to generate shore/river-style overlays from materials instead of hand-painting every edge variant: Tile Surgeon (Windows) does corridor + border blends for square/iso/hex — https://sprite-surgeon.itch.io/tile-surgeon · demo https://www.youtube.com/watch?v=LqhijXW_MXE
For pure pixel look, animating a few water frames still helps a lot (as others said).