Nothing at all revolutionary here, only took couple of hours, would make a good Introduction to Vertex Shaders type project:
1) Take a super simple Sine over time displacement equation;
2) Apply displacement to the y position of each vertex
3) In this case, since the water is not a separate mesh (optimizations), use the Size buffer as a flag to mask the effect onto only the water tile vertices;
4) Optional extra: give PreShadow.vert the same treatment so shadows are correctly calculated;
5) Sit back and enjoy a very basic vertex shader tweak.