Maybe you could create a program to just change all of a certain shade, in bulk, to another shade. I find all you need is to slide that colour picker scale and select the dot at the exact location it previously was at the original shade and you come out with: different colour, same tone. hehe
Or maybe you don't need the water to splash the land. You could just get the boat to stop before it reaches the land and have the player walk to the shore (the water's too shallow kind of thing). Then you only need to remove some pixels from the player sprite.
This also means you could have beaches and let players swim.
Maybe you could have an underwater world?