diff --git a/docs/history.rst b/docs/history.rst
index c381976c..a8609571 100644
--- a/docs/history.rst
+++ b/docs/history.rst
@@ -3,6 +3,7 @@ History
 
 Unreleased
 ----------
+- BUG: Preserve requested bounds when resampling merge inputs (#859)
 - ENH: Add write support for Zarr spatial and proj conventions
 
 0.22.0
diff --git a/rioxarray/merge.py b/rioxarray/merge.py
index f9d6212f..73192290 100644
--- a/rioxarray/merge.py
+++ b/rioxarray/merge.py
@@ -9,6 +9,8 @@
 import numpy
 from rasterio.crs import CRS
 from rasterio.merge import merge as _rio_merge
+from rasterio.transform import Affine
+from rasterio.windows import transform as _rio_window_transform
 from xarray import DataArray, Dataset, IndexVariable
 
 from rioxarray._spatial_utils import _get_nonspatial_coords, _make_coords
@@ -60,9 +62,10 @@ def read(self, window, out_shape, *args, **kwargs) -> numpy.ma.MaskedArray:
                 _, out_height, out_width = out_shape
             else:
                 out_height, out_width = out_shape
-            data_window = self._xds.rio.reproject(
-                self._xds.rio.crs,
-                transform=self.transform,
+            data_window = data_window.rio.reproject(
+                data_window.rio.crs,
+                transform=_rio_window_transform(window, self.transform)
+                * Affine.scale(window.width / out_width, window.height / out_height),
                 shape=(out_height, out_width),
             )
 
diff --git a/test/integration/test_integration_merge.py b/test/integration/test_integration_merge.py
index 8d148fcc..7b2b4701 100644
--- a/test/integration/test_integration_merge.py
+++ b/test/integration/test_integration_merge.py
@@ -1,15 +1,48 @@
 import os
 
+import numpy
 import pytest
 import xarray
 from numpy import nansum
-from numpy.testing import assert_almost_equal
+from numpy.testing import assert_almost_equal, assert_array_equal
+from rasterio.io import MemoryFile
+from rasterio.merge import merge as rio_merge
+from rasterio.transform import from_origin
 
 from rioxarray import open_rasterio
 from rioxarray.merge import merge_arrays, merge_datasets
 from test.conftest import TEST_INPUT_DATA_DIR
 
 
+@pytest.mark.parametrize("bounds", [None, (1, 1, 3, 3), (0.8, 0.6, 3.4, 3.2)])
+def test_merge_arrays__bounds(bounds):
+    data = numpy.arange(16, dtype=numpy.uint8).reshape(1, 4, 4)
+    transform = from_origin(0, 4, 1, 1)
+    array = (
+        xarray.DataArray(data, dims=("band", "y", "x"))
+        .rio.write_crs("EPSG:4326")
+        .rio.write_transform(transform)
+    )
+
+    with MemoryFile() as memory_file:
+        with memory_file.open(
+            driver="GTiff",
+            height=4,
+            width=4,
+            count=1,
+            dtype=data.dtype,
+            crs=array.rio.crs,
+            transform=transform,
+        ) as raster:
+            raster.write(data)
+            expected, expected_transform = rio_merge([raster], bounds=bounds)
+
+    merged = merge_arrays([array], bounds=bounds)
+
+    assert_array_equal(merged.values, expected)
+    assert merged.rio.transform() == expected_transform
+
+
 @pytest.mark.parametrize("squeeze", [True, False])
 def test_merge_arrays(squeeze):
     dem_test = os.path.join(TEST_INPUT_DATA_DIR, "MODIS_ARRAY.nc")