When needing to animate tilemap tiles, there are a few options. Creating sprites for just the parts you need animated works, like you said. You can also either layer the tilemaps and cycle through them by toggling visibility, or have the animation frames in the tileset and cycle through the tiles dynamically by events. Third way that may be more efficient if you have a highly dynamic coastline would be to maybe draw it at runtime using the drawing canvas plugin.
Finally, although I'm just theorycrafting at this point, I feel like you should be able to manage something with a low resolution static sprite in the shape of the coastline with a gradient, scale it, and use the alpha clamp effect to have it shrink and grow.