As allways I'm here to teach you a very very easy way for you to improve your water animations. In fact, it's so easy you don't have to do almost anything!
This tutorial is Beginner Friendly.
After the tutorial you'll have your water looking like this:


So Let's Start!
First Part - Applying the Effect
#1- Download the image below and put it inside the "Parallaxes" folder of your game:
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#5- Test to see how it looks!
Hope you enjoyed the Tutorial! :)
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Also hope you enjoy a little extra I put in the "Outside_A1" Graphic. A grass tile animation that makes it look like it's moving due to the wind.
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Second Part - How to do it?
#1- Make a caustic image that can be tileable. Like this one for example:

#1- Make a caustic image that can be tileable. Like this one for example:

#3- Loop the caustics image until it fills the size of the cloudy image. Collapse all the copies into one layer if needed.
#4- Reduce the opacity of the top layer until you are satisfied with the result.
#5- Now open the "Outside_A1" image and reduce the opacity to about 70% in the water tiles. So it will enable the Parallax graphic to mix with the water one to give the cool effect.
And voilá! Effect done.
Thank you for your time, and let me know what you think!
Busted Ed
You can view the effect happening in my demo "Busted Ed's Tips n Tricks" that can be found here:
http://forums.rpgmakerweb.com/index.php?/topic/19717-updated-bustededs-tips-n-tricks/