From directly above, the pond center shows dark green (0.12,0.12,0.08) — that's the grass/dirt, NOT water. The water disc is definitely not rendering. Even straight down at (8,-7,20), the center pixel is dark ground.

The water disc must be UNDER the ground mesh. Let me check: the ground mesh is one big grid with the pond depression carved in. But the depression function only dips to -1.19 at the exact center, and the rim at 0.35ish. The water disc at z=0.25 with radius 7 — the ground mesh at the pond area should be BELOW 0.25 over most of the depression. Unless... the ground mesh wasn't updated with the terrain function correctly? We saw vertices near the pond at -0.6 to -1.2, so the ground dips properly.

Wait — maybe the issue is the ground mesh has its own faces covering the water: the ground is a grid of 130x130 quads. When the terrain dips, the quads form a dish. The water disc is a flat circle at 0.25. The ground quad at the pond center is at -1.19, but the quad's EDGES might be higher, and the camera from above sees... no, from straight above at (8,-7,20) looking down, the first surface hit at the center is the water at 0.25 (if it exists) or the ground at -1.19. It shows ground, so water is not there.

Let me check if the water object has some modifier or is scaled weirdly, or its mesh data is actually elsewhere. Let me print the water object's matrix world and world-space vertex positions.

import bpy
import numpy as np

pond = bpy.data.objects['PondWater']
print('matrix', pond.matrix_world)
print('location', pond.location)
# world verts
ws = [pond.matrix_world @ v.co for v in pond.data.vertices]
ws = np.array([(v.x, v.y, v.z) for v in ws])
print('world x range', ws[:,0].min(), ws[:,0].max())
print('world y range', ws[:,1].min(), ws[:,1].max())
print('world z range', ws[:,2].min(), ws[:,2].max())
print('n verts', len(ws))
print('sample', ws[:3])

# is there a scale on the object?
print('scale', pond.scale)
# check ground vertex at (8,-7)
g = bpy.data.objects['Ground']
for v in g.data.vertices:
    if abs(v.co.x-8)<0.01 and abs(v.co.y+7)<0.01:
        print('ground vert at pond center', v.co)
        break
# find closest ground verts
import math
best = min(g.data.vertices, key=lambda v: (v.co.x-8)**2+(v.co.y+7)**2)
print('closest ground vert', best.co)