diff --git a/src/rail_cmd.cpp b/src/rail_cmd.cpp
--- a/src/rail_cmd.cpp
+++ b/src/rail_cmd.cpp
@@ -2930,6 +2930,14 @@ static CommandCost TestAutoslopeOnRailTi
 	return  cost;
 }
 
+/**
+ * Test-procedure for HasVehicleOnPos to check for a ship.
+ */
+static Vehicle *EnsureNoShipProc(Vehicle *v, void *data)
+{
+	return v->type == VEH_SHIP ? v : NULL;
+}
+
 static CommandCost TerraformTile_Track(TileIndex tile, DoCommandFlag flags, int z_new, Slope tileh_new)
 {
 	int z_old;
@@ -2939,6 +2947,9 @@ static CommandCost TerraformTile_Track(T
 		/* Is there flat water on the lower halftile that must be cleared expensively? */
 		bool was_water = (GetRailGroundType(tile) == RAIL_GROUND_WATER && IsSlopeWithOneCornerRaised(tileh_old));
 
+		/* Allow clearing the water only if there is no ship */
+		if (was_water && HasVehicleOnPos(tile, NULL, &EnsureNoShipProc)) return_cmd_error(STR_ERROR_SHIP_IN_THE_WAY);
+
 		/* First test autoslope. However if it succeeds we still have to test the rest, because non-autoslope terraforming is cheaper. */
 		CommandCost autoslope_result = TestAutoslopeOnRailTile(tile, flags, z_old, tileh_old, z_new, tileh_new, rail_bits);