The water material is fine. Let me check if the water disc might be underneath the ground mesh — the ground is a 130x130 grid (size 68) whose vertices follow the terrain. The water disc at z=0.25 covers only where terrain < 0.25. But the water disc is a flat circle at z=0.25 with radius 7 — at the pond edges the terrain rises above 0.25, so the disc's outer parts would be buried under the ground mesh. That's fine — the visible part is the depressed area.

But wait: the sample at pond center (8,-7) showed dirt. Let me check what the terrain does around (8,-7): -1.19, so the ground is 1.4 below water. The water should be clearly visible there. Unless the camera ray hits the water at a very grazing angle and the transmission makes it look like the bottom.

Let me render a small crop around the pond center and analyze the pixels there.

import bpy, os
import numpy as np
from mathutils import Vector
from bpy_extras.object_utils import world_to_camera_view

p = r"<home>\AppData\Local\Temp\check_render3.png"
img = bpy.data.images.load(p)
w, h = img.size
px = np.array(img.pixels[:], dtype=float).reshape((h, w, 4))[..., :3]

cam = bpy.data.objects['Camera']
scene = bpy.context.scene

def ndc(xyz):
    v = world_to_camera_view(scene, cam, Vector(xyz))
    return v.x, v.y

# scan the region around the pond center ndc (0.67,0.2) in a 200x200 window
cx, cy = ndc((8,-7,0.25))
col0, row0 = int(cx*w), int((1-cy)*h)
print('pond center px', (col0, row0))
region = px[max(0,row0-120):row0+120, max(0,col0-120):col0+120]
print('region mean', region.reshape(-1,3).mean(axis=0).round(3))
print('region min/max', region.reshape(-1,3).min(axis=0).round(3), region.reshape(-1,3).max(axis=0).round(3))

# Also check a wider band
band = px[max(0,row0-60):row0+60, :]
print('full-width band around pond row: mean', band.reshape(-1,3).mean(axis=0).round(3))
bpy.data.images.remove(img)