diff --git a/tests/models/abiotic/test_abiotic_tools.py b/tests/models/abiotic/test_abiotic_tools.py
index 2eb1f11eb..d7452cc10 100644
--- a/tests/models/abiotic/test_abiotic_tools.py
+++ b/tests/models/abiotic/test_abiotic_tools.py
@@ -338,9 +338,20 @@ def test_calculate_atmospheric_layer_geometry(
         layer_structure=lyr_str,
     )
 
-    for var in ["heights", "thickness", "layer_top", "layer_midpoints"]:
+    for var in ["heights", "thickness", "layer_midpoints"]:
         assert var in result
 
+    exp_heights = np.array(
+        [
+            [32.0, 32.0, 32.0, 32.0],
+            [30.0, 30.0, 30.0, np.nan],
+            [20.0, 20.0, np.nan, np.nan],
+            [10.0, np.nan, np.nan, np.nan],
+            [0.1, 0.1, 0.1, 0.1],
+        ]
+    )
+    np.testing.assert_allclose(result["heights"], exp_heights, rtol=1e-04, atol=1e-04)
+
     exp_thickness = np.array(
         [
             [2.0, 2.0, 2.0, 31.9],
@@ -356,11 +367,11 @@ def test_calculate_atmospheric_layer_geometry(
 
     exp_midpoints = np.array(
         [
-            [1.0, 1.0, 1.0, 15.95],
-            [7.0, 7.0, 16.95, np.nan],
-            [17, 21.95, np.nan, np.nan],
-            [26.95, np.nan, np.nan, np.nan],
-            [31.95, 31.95, 31.95, 31.95],
+            [31.0, 31.0, 31.0, 16.05],
+            [25.0, 25.0, 15.05, np.nan],
+            [15.0, 10.05, np.nan, np.nan],
+            [5.05, np.nan, np.nan, np.nan],
+            [0.05, 0.05, 0.05, 0.05],
         ]
     )
 
diff --git a/virtual_ecosystem/models/abiotic/abiotic_tools.py b/virtual_ecosystem/models/abiotic/abiotic_tools.py
index 47383d648..015a5191d 100644
--- a/virtual_ecosystem/models/abiotic/abiotic_tools.py
+++ b/virtual_ecosystem/models/abiotic/abiotic_tools.py
@@ -305,10 +305,9 @@ def update_profile_from_reference(
 
 
 def calculate_atmospheric_layer_geometry(data: Data, layer_structure: LayerStructure):
-    """Calculate heights, thickness, layer tops, and midpoints for atmospheric layers.
+    """Calculate heights, layer thickness, and midpoints for atmospheric layers.
 
-    The layer top and midpoint values are distances in metres below the above canopy
-    reference height for each cell.
+    The midpoint values are distances in metres above ground for each cell.
 
     Args:
         data: Data object
@@ -324,17 +323,13 @@ def calculate_atmospheric_layer_geometry(data: Data, layer_structure: LayerStruc
     # Compute thickness
     thickness = compute_layer_thickness_for_varying_canopy(heights=heights)
 
-    # Compute the top of each layer below the above canopy reference height
-    layer_top = np.abs(heights - heights[0, :])
-
-    # Compute the midpoint of each layer as the distance below the above canopy
-    # reference height
-    midpoints = layer_top + thickness / 2
+    # Compute the midpoint of each layer as the height above ground minus half the layer
+    # thickness
+    midpoints = heights - thickness / 2
 
     return {
         "heights": heights,
         "thickness": thickness,
-        "layer_top": layer_top,
         "layer_midpoints": midpoints,
     }