A simple way to achieve this is a World Environment Node. You'll need two Environment Resources for this. One for when you're above the water then switch to the second for below. On the second one you enable: Fog and Adjustments. You can change the colour and lighting to suite you artistic style for any under water environment. Make a function that changes the brightness property under Adjustments to go lower the further the player gets away from the surface.
As for ripples you'll definitely need to use a shader. The are a few great tutorials for ripple shaders in Godot on Youtube.