Easy way to make a custom toon water shader

Alrighty then! Here's how I made a pretty similar effect in Unity:

Step 1: create a plane, re-size it to whatever you want. (or use a mesh/gameobject)

Step 2: assign your water texture to the plane Example (Make the material "Unlit/Texture")

Step 3: tile the texture a bit (til you're happy with it) and add this script:

 using UnityEngine;
 using System.Collections;
  
 public class AnimatedUVs : MonoBehaviour 
 {
     public int materialIndex = 0;
     public Vector2 uvAnimationRate = new Vector2( 1.0f, 0.0f );
     public string textureName = "_MainTex";
  
     Vector2 uvOffset = Vector2.zero;
  
     void LateUpdate() 
     {
         uvOffset += ( uvAnimationRate * Time.deltaTime );
         if( renderer.enabled )
         {
             renderer.materials[ materialIndex ].SetTextureOffset( textureName, uvOffset );
         }
     }
 }

Step 4: set the animation of the texture to "0.05" in any direction you want (It will roll smoothly)

If you want the mesh to deform into waves, then you might want to look into noise deformation to deform the plane.

So, this is as close as I can get to the wind waker water effects. I hope it helps! :D