water shader and mesh

I was working on this project to pass the time and keep my mind occupied and the backend scripting engine part is done mostly (the how things work part), so I eventually started to look into 'the how things look' part, and as this is uncharted territory for me, it's time to pop my first question.

I converted the visual level from the original toolset/game into XML, and then randomly picked a water mesh, I guess would be the correct terminology. I happily parsed the mesh from XML into unity, and created a solid shader, to make sure that whatever I did was right. And it looks that it's okay. As you can see in the picture, the 'water' is green. and now I would like to turn the water into something that resembles it, but for some reason when actually turn it into water, the water is actually everywhere like a square, doesn't follow the 'green' triangles

So that's my question: how can I make only the green be water, and the gray just transparent nothing?

thank you very much, and I apologize if this is a noob question with a very simple answer...

below is a sample of how the original format looks like once converted to XML, in case you curious

 <?xml version="1.0" encoding="utf-8" standalone="yes"?>
 <gff4 type="TRN" version="V3.1" platform="PC">
   <struct name="WAT ">
     <struct name="WATR" label="7900" alias="WaterInformation">
       <uint32 label="7901" alias="WaterVersion">1</uint32>
       <sint32 label="7902" alias="WaterID">6523</sint32>
       <struct_list label="7903" alias="WaterVertexList">
         <struct name="VERT" index="0">
           <vector3f label="7904" alias="WaterVertexPosition">
             <float>0.000000</float><float>0.000000</float><float>0.000000</float>
           </vector3f>
           <vector3f label="7905" alias="WaterVertexNormal">
             <float>0.000000</float><float>0.000000</float><float>1.000000</float>
           </vector3f>
           <vector3f label="7906" alias="WaterVertexUVW">
             <float>0.000000</float><float>1.000000</float><float>0.000000</float>
           </vector3f>
           <color4f label="7907" alias="WaterVertexColor">
             <float>0.640000</float><float>0.460000</float><float>0.410000</float><float>-2.411328</float>
           </color4f>
         </struct>
       </struct_list>
       <uint32_list label="7908" alias="WaterVertexIndexList">
         <uint32 index="0">0</uint32>
         <uint32 index="1">1</uint32>
         <uint32 index="2">2</uint32>
         <uint32 index="3">0</uint32>
         <uint32 index="4">2</uint32>
         <uint32 index="4">3</uint32>
       </uint32_list>
     </struct>
   </struct>
 </gff4>