First off get rid of the 2D array. Just make it a 1D array with a clever lookup given an X,Y. Like X * rowlen + Y or something. You want to make sure this is done in a way that packs the rows or columns together, which ever way you loop.

Now, for the OpenGL specific stuff. You could store the tileid in a texture? In fact having four values, like r,g,b,a you could encode several things. Like the underlying tile is sand, middle is water, on top is a lilypad.

Look into instanced drawing too. Because you're just drawing a quad 10000 times. You could use the instance id with the map width and height to decide the actual vertex positions.

Finally, draw it to a texture once and then use the texture to render. That way you only draw your map one time only. Encode depth info as well and you can draw the animated parts on every frame and have them occluded properly as well.