diff --git a/pygmt/tests/test_io.py b/pygmt/tests/test_io.py
index 447e853ff54..333fbda0f3d 100644
--- a/pygmt/tests/test_io.py
+++ b/pygmt/tests/test_io.py
@@ -14,8 +14,9 @@ def test_io_load_dataarray():
     GMTDataArrayAccessor information loaded.
     """
     with GMTTempFile(suffix=".nc") as tmpfile:
+        rng = np.random.default_rng()
         grid = xr.DataArray(
-            data=np.random.rand(2, 2), coords=[[0.1, 0.2], [0.3, 0.4]], dims=("x", "y")
+            data=rng.random((2, 2)), coords=[[0.1, 0.2], [0.3, 0.4]], dims=("x", "y")
         )
         grid.to_netcdf(tmpfile.name)
         dataarray = load_dataarray(tmpfile.name)
diff --git a/pygmt/tests/test_x2sys_cross.py b/pygmt/tests/test_x2sys_cross.py
index a287d31ce93..fc5e1e1ac83 100644
--- a/pygmt/tests/test_x2sys_cross.py
+++ b/pygmt/tests/test_x2sys_cross.py
@@ -110,15 +110,15 @@ def test_x2sys_cross_input_two_dataframes(mock_x2sys_home):
         # Create pandas.DataFrame track tables
         tracks = []
         for i in range(2):
-            np.random.seed(seed=i)
-            track = pd.DataFrame(data=np.random.rand(10, 3), columns=("x", "y", "z"))
+            rng = np.random.default_rng(seed=i)
+            track = pd.DataFrame(data=rng.random((10, 3)), columns=("x", "y", "z"))
             track["time"] = pd.date_range(start=f"2020-{i}1-01", periods=10, freq="min")
             tracks.append(track)
 
         output = x2sys_cross(tracks=tracks, tag=tag, coe="e")
 
         assert isinstance(output, pd.DataFrame)
-        assert output.shape == (30, 12)
+        assert output.shape == (26, 12)
         columns = list(output.columns)
         assert columns[:6] == ["x", "y", "t_1", "t_2", "dist_1", "dist_2"]
         assert columns[6:] == ["head_1", "head_2", "vel_1", "vel_2", "z_X", "z_M"]
@@ -160,16 +160,16 @@ def test_x2sys_cross_input_two_filenames(mock_x2sys_home):
 
         # Create temporary xyz files
         for i in range(2):
-            np.random.seed(seed=i)
+            rng = np.random.default_rng(seed=i)
             with open(
                 os.path.join(os.getcwd(), f"track_{i}.xyz"), mode="w", encoding="utf8"
             ) as fname:
-                np.savetxt(fname=fname, X=np.random.rand(10, 3))
+                np.savetxt(fname=fname, X=rng.random((10, 3)))
 
         output = x2sys_cross(tracks=["track_0.xyz", "track_1.xyz"], tag=tag, coe="e")
 
         assert isinstance(output, pd.DataFrame)
-        assert output.shape == (24, 12)
+        assert output.shape == (18, 12)
         columns = list(output.columns)
         assert columns[:6] == ["x", "y", "i_1", "i_2", "dist_1", "dist_2"]
         assert columns[6:] == ["head_1", "head_2", "vel_1", "vel_2", "z_X", "z_M"]