In this case Tiled. But I can use something else. If all is ok in the tiles - it is my fault and I will have to think of something else. :) Thank you very much for your time and for your work.
This pack when I made it was for RPGMaker VX/VXAce which have a special way of animating the water tiles. You could look at how those pieces of software handle it to see.
Thank you very much. Will look into it. :)