diff --git a/AFQ/api/participant.py b/AFQ/api/participant.py
index b5a6e4458..09c3d05eb 100644
--- a/AFQ/api/participant.py
+++ b/AFQ/api/participant.py
@@ -15,7 +15,7 @@
 from AFQ.tasks.segmentation import get_segmentation_plan
 from AFQ.tasks.viz import get_viz_plan
 from AFQ.utils.path import drop_extension
-from AFQ.data.s3bids import read_json
+from AFQ.data.utils import read_json
 
 
 __all__ = ["ParticipantAFQ"]
diff --git a/AFQ/data/s3bids.py b/AFQ/data/s3bids.py
index 65a6d2d20..e03428366 100644
--- a/AFQ/data/s3bids.py
+++ b/AFQ/data/s3bids.py
@@ -11,7 +11,6 @@
 from dask.diagnostics import ProgressBar
 
 from pathlib import Path
-import os
 import os.path as op
 
 import logging
@@ -24,10 +23,41 @@
 from bids import BIDSLayout
 from AFQ.data.fetch import to_bids_description
 
+import warnings
+import functools
+
+
+# +---------------------+
+# | Deprecation helpers |
+# +---------------------+
+def deprecate_function(func):
+    @functools.wraps(func)
+    def new_func(*args, **kwargs):
+        msg = f"The function {func.__name__} is part of the "
+        msg += "AFQ.data.s3bids module, which will be removed "
+        msg += "in version 2.0 of pyAFQ."
+        warnings.warn(msg, DeprecationWarning, stacklevel=2)
+        return func(*args, **kwargs)
+
+    return new_func
+
+
+def deprecate_class(klass):
+    class new_klass(klass):
+        def __init__(self, *args, **kwargs):
+            msg = f"The class {klass.__name__} is part of the "
+            msg += "AFQ.data.s3bids module, which will be removed "
+            msg += "in version 2.0 of pyAFQ."
+            warnings.warn(msg, DeprecationWarning, stacklevel=2)
+
+            return klass.__init__(*args, **kwargs)
+    return new_klass
+
 
 # +----------------------------------------------------+
 # | Begin S3BIDSStudy classes and supporting functions |
 # +----------------------------------------------------+
+@deprecate_function
 def get_s3_client(anon=True):
     """Return a boto3 s3 client
 
@@ -193,6 +223,7 @@ def _download_from_s3(fname, bucket, key, overwrite=False, anon=True):
         fs.get("/".join([bucket, key]), fname)
 
 
+@deprecate_class
 class S3BIDSSubject:
     """A single study subject hosted on AWS S3"""
 
@@ -442,6 +473,7 @@ def split_key(key):
             progress.close()
 
 
+@deprecate_class
 class HBNSubject(S3BIDSSubject):
     """A subject in the HBN study
 
@@ -525,6 +557,7 @@ def get_deriv_type(s3_key):
         self._s3_keys = s3_keys
 
 
+@deprecate_class
 class S3BIDSStudy:
     """A BIDS-compliant study hosted on AWS S3"""
 
@@ -953,6 +986,7 @@ def download(self, directory,
         compute(*results, scheduler='threads')
 
 
+@deprecate_class
 class HBNSite(S3BIDSStudy):
     """An HBN study site
 
@@ -1184,6 +1218,7 @@ def s3fs_nifti_write(img, fname, fs=None):
         ff.write(data)
 
 
+@deprecate_function
 def s3fs_nifti_read(fname, fs=None, anon=False):
     """
     Lazily reads a nifti image from S3.
@@ -1222,44 +1257,7 @@ def s3fs_nifti_read(fname, fs=None, anon=False):
     return img
 
 
-def write_json(fname, data):
-    """
-    Write data to JSON file.
-
-    Parameters
-    ----------
-    fname : str
-        Full path to the file to write.
-
-    data : dict
-        A dict containing the data to write.
-
-    Returns
-    -------
-    None
-    """
-    with open(fname, 'w') as ff:
-        json.dump(data, ff, default=lambda obj: "Not Serializable")
-
-
-def read_json(fname):
-    """
-    Read data from a JSON file.
-
-    Parameters
-    ----------
-    fname : str
-        Full path to the data-containing file
-
-    Returns
-    -------
-    dict
-    """
-    with open(fname, 'r') as ff:
-        out = json.load(ff)
-    return out
-
-
+@deprecate_function
 def s3fs_json_read(fname, fs=None, anon=False):
     """
     Reads json directly from S3
@@ -1283,6 +1281,7 @@ def s3fs_json_read(fname, fs=None, anon=False):
     return data
 
 
+@deprecate_function
 def s3fs_json_write(data, fname, fs=None):
     """
     Writes json from a dict directly into S3
diff --git a/AFQ/data/utils.py b/AFQ/data/utils.py
index 43913c7a9..116d8bd92 100644
--- a/AFQ/data/utils.py
+++ b/AFQ/data/utils.py
@@ -1,3 +1,5 @@
+import json
+
 BUNDLE_RECO_2_AFQ = \
     {
         "AF_L": "ARC_L", "AF_R": "ARC_R",
@@ -31,3 +33,41 @@
      'RightILF': 'ILF_R', 'LeftILF': 'ILF_L',
      'Right SLF': 'SLF_R', 'Left SLF': 'SLF_L',
      'RightSLF': 'SLF_R', 'LeftSLF': 'SLF_L'}
+
+
+def write_json(fname, data):
+    """
+    Write data to JSON file.
+
+    Parameters
+    ----------
+    fname : str
+        Full path to the file to write.
+
+    data : dict
+        A dict containing the data to write.
+
+    Returns
+    -------
+    None
+    """
+    with open(fname, 'w') as ff:
+        json.dump(data, ff, default=lambda obj: "Not Serializable")
+
+
+def read_json(fname):
+    """
+    Read data from a JSON file.
+
+    Parameters
+    ----------
+    fname : str
+        Full path to the data-containing file
+
+    Returns
+    -------
+    dict
+    """
+    with open(fname, 'r') as ff:
+        out = json.load(ff)
+    return out
diff --git a/AFQ/definitions/mapping.py b/AFQ/definitions/mapping.py
index 2d2a15a1c..3205c22dc 100644
--- a/AFQ/definitions/mapping.py
+++ b/AFQ/definitions/mapping.py
@@ -7,7 +7,7 @@
 from AFQ.definitions.utils import Definition, find_file
 from dipy.align import syn_registration, affine_registration
 import AFQ.registration as reg
-import AFQ.data.s3bids as afs
+from AFQ.data.utils import write_json
 from AFQ.tasks.utils import get_fname
 
 from dipy.align.imaffine import AffineMap
@@ -320,7 +320,7 @@ def prealign(self, base_fname, reg_subject, reg_template, save=True):
             np.save(prealign_file, aff)
             meta_fname = get_fname(
                 base_fname, f'{prealign_file_desc}.json')
-            afs.write_json(meta_fname, meta)
+            write_json(meta_fname, meta)
         return prealign_file if save else np.load(prealign_file)
 
     def get_for_subses(self, base_fname, dwi, bids_info, reg_subject,
@@ -350,7 +350,7 @@ def get_for_subses(self, base_fname, dwi, bids_info, reg_subject,
                 meta["dependent"] = "dwi"
             else:
                 meta["dependent"] = "trk"
-            afs.write_json(meta_fname, meta)
+            write_json(meta_fname, meta)
         reg_prealign_inv = np.linalg.inv(reg_prealign) if self.use_prealign\
             else None
         mapping = reg.read_mapping(
diff --git a/AFQ/tasks/decorators.py b/AFQ/tasks/decorators.py
index 3a6c23652..65f233bcb 100644
--- a/AFQ/tasks/decorators.py
+++ b/AFQ/tasks/decorators.py
@@ -7,7 +7,7 @@
 import nibabel as nib
 from dipy.io.streamline import save_tractogram
 from dipy.io.stateful_tractogram import StatefulTractogram
-from AFQ.data.s3bids import write_json
+from AFQ.data.utils import write_json
 
 import numpy as np
 
diff --git a/AFQ/tasks/mapping.py b/AFQ/tasks/mapping.py
index 99f79a748..7e8916e5d 100644
--- a/AFQ/tasks/mapping.py
+++ b/AFQ/tasks/mapping.py
@@ -8,7 +8,7 @@
 from AFQ.tasks.decorators import as_file
 from AFQ.tasks.utils import get_fname, with_name, str_to_desc
 import AFQ.data.fetch as afd
-from AFQ.data.s3bids import write_json
+from AFQ.data.utils import write_json
 from AFQ.utils.path import drop_extension
 import AFQ.utils.volume as auv
 from AFQ.definitions.mapping import SynMap
diff --git a/AFQ/tasks/segmentation.py b/AFQ/tasks/segmentation.py
index 3fc54e5d7..7e0c845e0 100644
--- a/AFQ/tasks/segmentation.py
+++ b/AFQ/tasks/segmentation.py
@@ -14,7 +14,7 @@
 from AFQ.utils.path import drop_extension
 import AFQ.utils.streamlines as aus
 from AFQ.tasks.utils import get_default_args
-from AFQ.data.s3bids import write_json
+from AFQ.data.utils import write_json
 import AFQ.api.bundle_dict as abd
 import AFQ.utils.streamlines as aus
 import AFQ.utils.volume as auv
diff --git a/AFQ/tasks/viz.py b/AFQ/tasks/viz.py
index be0f04726..e2a56add7 100644
--- a/AFQ/tasks/viz.py
+++ b/AFQ/tasks/viz.py
@@ -12,7 +12,7 @@
 
 from AFQ.tasks.utils import get_fname, with_name, str_to_desc
 import AFQ.utils.volume as auv
-from AFQ.data.s3bids import write_json
+from AFQ.data.utils import write_json
 from AFQ.viz.utils import Viz
 
 from plotly.subplots import make_subplots
diff --git a/AFQ/utils/streamlines.py b/AFQ/utils/streamlines.py
index f35129f6d..e54ea30e3 100644
--- a/AFQ/utils/streamlines.py
+++ b/AFQ/utils/streamlines.py
@@ -2,7 +2,7 @@
 from dipy.io.streamline import load_tractogram
 import numpy as np
 from dipy.io.stateful_tractogram import StatefulTractogram, Space
-from AFQ.data.s3bids import read_json
+from AFQ.data.utils import read_json
 import os.path as op
 
 from AFQ.utils.path import drop_extension