Using water as green screen so I had this idea but inorder to do it, I need to have water as a green screen. (Because I wanted to make the image move like water). So I was thinking of using dye to color the water and key that color out in premiere pro but its not working that well.
Is there any alternative to this. Or  even an effect in premiere or after effect that let's you move images like the flow of water?
Take a look at using noise turbulence to displace the image. You can do this in after effects. There are lots of good tutorials on it. I recommend this one:

                
            
Maybe add some images so we can see what you have and what you’re going for.