Shader "Custom/WaterMask"
{
  SubShader
  {
    Pass
    {
      // Render the mask after regular geometry, but before masked geometry and
      // transparent things.
      // You may need to adjust the queue value depending on your setup
      Tags {"RenderType"="Opaque" "Queue"="Geometry+10" "IgnoreProjector"="True" }
      // Don't draw in the RGBA channels; just the depth buffer
      // This is important for making our mask mesh invisible
      ColorMask 0
      // We write to the depth buffer which will hide the water below our mask mesh
      ZWrite On
      // We don't want anything to draw in front of our mask,
      // as it would allow the water to then be drawn on top of us
      ZTest Off
    }
  }
}

Shader "Custom/WaterMask"
{
  SubShader
  {
    Pass
    {
      // Render the mask after regular geometry, but before masked geometry and
      // transparent things.
      // You may need to adjust the queue value depending on your setup
      Tags {"RenderType"="Opaque" "Queue"="Geometry+10" "IgnoreProjector"="True" }
      // Don't draw in the RGBA channels; just the depth buffer
      // This is important for making our mask mesh invisible
      ColorMask 0
      // Writing to z depth isn't necessarily required, but might hide
      // any extra effects your water has like caustics when the boat interior is below the water surface
      ZWrite On
      // We don't want anything to draw in front of our mask,
      // as it would allow the water to then be drawn on top of us
      ZTest Off
      // The real meat of the solution.
      // Ref - The value this stencil operation is in reference to. I arbitrarily picked '1'.
      // Comp - The comparison method for deciding whether to draw a pixel.
      //        For drawing the mask, we always want it to render regardless of the
      //        stencil state, so I chose 'always'
      // Pass - What to do with the stencil state after drawing a pixel. I chose 'replace',
      //        which means that whatever was in the stencil buffer will be replaced with '1'
      //        where our mask is drawn.
      Stencil
      {
        Ref 1
        Comp always
        Pass replace
      }
    }
  }
}

Pass
{
  ZWrite On
  // Mask the water using the stencil buffer
  Stencil
  {
    Ref 1
    Comp notequal
    Pass keep
  }
  CGPROGRAM
  #pragma vertex waterVert
  #pragma fragment waterFrag
  ENDCG
}