diff --git a/borgmatic/commands/arguments.py b/borgmatic/commands/arguments.py
index e95ec5f4..b09c5660 100644
--- a/borgmatic/commands/arguments.py
+++ b/borgmatic/commands/arguments.py
@@ -1,5 +1,7 @@
 import collections
 import itertools
+import json
+import re
 import sys
 from argparse import ArgumentParser
 
@@ -282,12 +284,155 @@ def parse_arguments_for_actions(unparsed_arguments, action_parsers, global_parse
     )
 
 
-def make_parsers():
+def add_arguments_from_schema(arguments_group, schema, unparsed_arguments, names=None):
     '''
-    Build a global arguments parser, individual action parsers, and a combined parser containing
-    both. Return them as a tuple. The global parser is useful for parsing just global arguments
-    while ignoring actions, and the combined parser is handy for displaying help that includes
-    everything: global flags, a list of actions, etc.
+    Given an argparse._ArgumentGroup instance, a configuration schema dict, and a sequence of
+    unparsed argument strings, convert the entire schema into corresponding command-line flags and
+    add them to the arguments group.
+
+    For instance, given a schema of:
+
+        {
+            'type': 'object',
+            'properties': {
+                'foo': {
+                    'type': 'object',
+                    'properties': {
+                        'bar': {'type': 'integer'}
+                    }
+                }
+            }
+        }
+
+    ... the following flag will be added to the arguments group:
+
+        --foo.bar
+
+    If "foo" is instead an array of objects, it will get added like this
+
+        --foo[0].bar
+
+    And if names are also passed in, they are considered to be the name components of an option
+    (e.g. "foo" and "bar") and are used to construct a resulting flag.
+    '''
+    if names is None:
+        names = ()
+
+    schema_type = schema.get('type')
+
+    # If this option has multiple types, just use the first one (that isn't "null").
+    if isinstance(schema_type, list):
+        try:
+            schema_type = next(single_type for single_type in schema_type if single_type != 'null')
+        except StopIteration:
+            raise ValueError(f'Unknown type in configuration schema: {schema_type}')
+
+    # If this is an "object" type, recurse for each child option ("property").
+    if schema_type in {'object', 'array'}:
+        properties = (
+            schema.get('items', {}).get('properties')
+            if schema_type == 'array'
+            else schema.get('properties')
+        )
+
+        if properties:
+            for name, child in properties.items():
+                add_arguments_from_schema(
+                    arguments_group,
+                    child,
+                    unparsed_arguments,
+                    names + ((name + '[0]',) if child.get('type') == 'array' else (name,)),
+                )
+
+        return
+
+    flag_name = '.'.join(names)
+    description = schema.get('description')
+    metavar = names[-1].upper()
+
+    if schema_type == 'array':
+        metavar = metavar.rstrip('S')
+
+    if description:
+        if schema_type == 'array':
+            items_schema = schema.get('items', {})
+
+            description += ' Can specify flag multiple times.'
+
+        if '[0]' in flag_name:
+            description += ' To specify a different list element, replace the "[0]" with another array index ("[1]", "[2]", etc.).'
+
+        description = description.replace('%', '%%')
+
+    try:
+        argument_type = {'string': str, 'integer': int, 'boolean': bool, 'array': str}[schema_type]
+    except KeyError:
+        raise ValueError(f'Unknown type in configuration schema: {schema_type}')
+
+    arguments_group.add_argument(
+        f"--{flag_name.replace('_', '-')}",
+        type=argument_type,
+        metavar=metavar,
+        action='append' if schema_type == 'array' else None,
+        help=description,
+    )
+
+    # We want to support flags that can have arbitrary indices like:
+    #
+    #   --foo.bar[1].baz
+    #
+    # But argparse doesn't support that natively because the index can be an arbitrary number. We
+    # won't let that stop us though, will we? So, if the current flag name has an array component in
+    # it (e.g. a name with "[0]"), then make a pattern that would match the flag name regardless of
+    # the number that's in it. The idea is that we want to look for unparsed arguments that appear
+    # like the flag name, but instead of "[0]" they have, say, "[1]" or "[123]".
+    #
+    # Next, we check each unparsed argument against that pattern. If one of them matches, add an
+    # argument flag for it to the argument parser group. Example:
+    #
+    # Let's say flag_name is:
+    #
+    #     --foo.bar[0].baz
+    #
+    # ... then the regular expression pattern will be:
+    #
+    #     ^--foo\.bar\[\d+\]\.baz
+    #
+    # ... and, if that matches an unparsed argument of:
+    #
+    #     --foo.bar[1].baz
+    #
+    # ... then an argument flag will get added equal to that unparsed argument. And the unparsed
+    # argument will match it when parsing is performed! In this manner, we're using the actual user
+    # CLI input to inform what exact flags we support!
+    if '[0]' not in flag_name or '--help' in unparsed_arguments:
+        return
+
+    pattern = re.compile(f'^--{flag_name.replace("[0]", r"\[\d+\]").replace(".", r"\.")}$')
+    existing_flags = set(
+        itertools.chain(
+            *(group_action.option_strings for group_action in arguments_group._group_actions)
+        )
+    )
+
+    for unparsed in unparsed_arguments:
+        unparsed_flag_name = unparsed.split('=', 1)[0]
+
+        if pattern.match(unparsed_flag_name) and unparsed_flag_name not in existing_flags:
+            arguments_group.add_argument(
+                unparsed_flag_name,
+                type=argument_type,
+                metavar=metavar,
+                help=description,
+            )
+
+
+def make_parsers(schema, unparsed_arguments):
+    '''
+    Given a configuration schema dict, build a global arguments parser, individual action parsers,
+    and a combined parser containing both. Return them as a tuple. The global parser is useful for
+    parsing just global arguments while ignoring actions, and the combined parser is handy for
+    displaying help that includes everything: global flags, a list of actions, etc.
     '''
     config_paths = collect.get_default_config_paths(expand_home=True)
     unexpanded_config_paths = collect.get_default_config_paths(expand_home=False)
@@ -388,6 +533,7 @@ def make_parsers():
         action='store_true',
         help='Display installed version number of borgmatic and exit',
     )
+    add_arguments_from_schema(global_group, schema, unparsed_arguments)
 
     global_plus_action_parser = ArgumentParser(
         description='''
@@ -1523,15 +1669,18 @@ def make_parsers():
     return global_parser, action_parsers, global_plus_action_parser
 
 
-def parse_arguments(*unparsed_arguments):
+def parse_arguments(schema, *unparsed_arguments):
     '''
-    Given command-line arguments with which this script was invoked, parse the arguments and return
-    them as a dict mapping from action name (or "global") to an argparse.Namespace instance.
+    Given a configuration schema dict and the command-line arguments with which this script was
+    invoked, parse the arguments and return them as a dict mapping from action name (or "global") to
+    an argparse.Namespace instance.
 
     Raise ValueError if the arguments cannot be parsed.
     Raise SystemExit with an error code of 0 if "--help" was requested.
     '''
-    global_parser, action_parsers, global_plus_action_parser = make_parsers()
+    global_parser, action_parsers, global_plus_action_parser = make_parsers(
+        schema, unparsed_arguments
+    )
     arguments, remaining_action_arguments = parse_arguments_for_actions(
         unparsed_arguments, action_parsers.choices, global_parser
     )
diff --git a/borgmatic/commands/borgmatic.py b/borgmatic/commands/borgmatic.py
index 5691df71..9cffbdf8 100644
--- a/borgmatic/commands/borgmatic.py
+++ b/borgmatic/commands/borgmatic.py
@@ -8,6 +8,8 @@ import time
 from queue import Queue
 from subprocess import CalledProcessError
 
+import ruamel.yaml
+
 import borgmatic.actions.borg
 import borgmatic.actions.break_lock
 import borgmatic.actions.change_passphrase
@@ -33,6 +35,7 @@ import borgmatic.actions.restore
 import borgmatic.actions.transfer
 import borgmatic.commands.completion.bash
 import borgmatic.commands.completion.fish
+import borgmatic.config.load
 from borgmatic.borg import umount as borg_umount
 from borgmatic.borg import version as borg_version
 from borgmatic.commands.arguments import parse_arguments
@@ -570,14 +573,14 @@ def run_actions(
                     )
 
 
-def load_configurations(config_filenames, overrides=None, resolve_env=True):
+def load_configurations(config_filenames, global_arguments, overrides=None, resolve_env=True):
     '''
-    Given a sequence of configuration filenames, a sequence of configuration file override strings
-    in the form of "option.suboption=value", and whether to resolve environment variables, load and
-    validate each configuration file. Return the results as a tuple of: dict of configuration
-    filename to corresponding parsed configuration, a sequence of paths for all loaded configuration
-    files (including includes), and a sequence of logging.LogRecord instances containing any parse
-    errors.
+    Given a sequence of configuration filenames, global arguments as an argparse.Namespace, a
+    sequence of configuration file override strings in the form of "option.suboption=value", and
+    whether to resolve environment variables, load and validate each configuration file. Return the
+    results as a tuple of: dict of configuration filename to corresponding parsed configuration, a
+    sequence of paths for all loaded configuration files (including includes), and a sequence of
+    logging.LogRecord instances containing any parse errors.
 
     Log records are returned here instead of being logged directly because logging isn't yet
     initialized at this point! (Although with the Delayed_logging_handler now in place, maybe this
@@ -605,6 +608,7 @@ def load_configurations(config_filenames, overrides=None, resolve_env=True):
             configs[config_filename], paths, parse_logs = validate.parse_configuration(
                 config_filename,
                 validate.schema_filename(),
+                global_arguments,
                 overrides,
                 resolve_env,
             )
@@ -928,9 +932,17 @@ def exit_with_help_link():  # pragma: no cover
 def main(extra_summary_logs=[]):  # pragma: no cover
     configure_signals()
     configure_delayed_logging()
+    schema_filename = validate.schema_filename()
 
     try:
-        arguments = parse_arguments(*sys.argv[1:])
+        schema = borgmatic.config.load.load_configuration(schema_filename)
+    except (ruamel.yaml.error.YAMLError, RecursionError) as error:
+        configure_logging(logging.CRITICAL)
+        logger.critical(error)
+        exit_with_help_link()
+
+    try:
+        arguments = parse_arguments(schema, *sys.argv[1:])
     except ValueError as error:
         configure_logging(logging.CRITICAL)
         logger.critical(error)
@@ -953,10 +965,10 @@ def main(extra_summary_logs=[]):  # pragma: no cover
         print(borgmatic.commands.completion.fish.fish_completion())
         sys.exit(0)
 
-    validate = bool('validate' in arguments)
     config_filenames = tuple(collect.collect_config_filenames(global_arguments.config_paths))
     configs, config_paths, parse_logs = load_configurations(
         config_filenames,
+        global_arguments,
         global_arguments.overrides,
         resolve_env=global_arguments.resolve_env and not validate,
     )
diff --git a/borgmatic/config/arguments.py b/borgmatic/config/arguments.py
new file mode 100644
index 00000000..96a28b4d
--- /dev/null
+++ b/borgmatic/config/arguments.py
@@ -0,0 +1,137 @@
+import io
+import re
+
+import ruamel.yaml
+
+
+LIST_INDEX_KEY_PATTERN = re.compile(r'^(?P<list_name>[a-zA-z-]+)\[(?P<index>\d+)\]$')
+
+
+def set_values(config, keys, value):
+    '''
+    Given a configuration dict, a sequence of parsed key strings, and a string value, descend into
+    the configuration hierarchy based on the keys to set the value into the right place.
+    '''
+    if not keys:
+        return
+
+    first_key = keys[0]
+
+    # Support "name[0]"-style list index syntax.
+    match = LIST_INDEX_KEY_PATTERN.match(first_key)
+
+    if match:
+        list_key = match.group('list_name')
+        list_index = int(match.group('index'))
+
+        if len(keys) == 1:
+            config[list_key][list_index] = value
+
+            return
+
+        if list_key not in config:
+            config[list_key] = []
+
+        try:
+            set_values(config[list_key][list_index], keys[1:], value)
+        except IndexError:
+            raise ValueError(f'The list index {first_key} is out of range')
+
+        return
+
+    if len(keys) == 1:
+        config[first_key] = value
+        return
+
+    if first_key not in config:
+        config[first_key] = {}
+
+    set_values(config[first_key], keys[1:], value)
+
+
+def type_for_option(schema, option_keys):
+    '''
+    Given a configuration schema dict and a sequence of keys identifying a potentially nested
+    option, e.g. ('extra_borg_options', 'create'), return the schema type of that option as a
+    string.
+
+    Return None if the option or its type cannot be found in the schema.
+    '''
+    option_schema = schema
+
+    for key in option_keys:
+        # Support "name[0]"-style list index syntax.
+        match = LIST_INDEX_KEY_PATTERN.match(key)
+
+        try:
+            if match:
+                option_schema = option_schema['properties'][match.group('list_name')]['items']
+            else:
+                option_schema = option_schema['properties'][key]
+        except KeyError:
+            return None
+
+    try:
+        return option_schema['type']
+    except KeyError:
+        return None
+
+
+def prepare_arguments_for_config(global_arguments, schema):
+    '''
+    Given global arguments as an argparse.Namespace and a configuration schema dict, parse each
+    argument that corresponds to an option in the schema and return a sequence of tuples (keys,
+    values) for that option, where keys is a sequence of strings. For instance, given the following
+    arguments:
+
+        argparse.Namespace(**{'my_option.sub_option': 'value1', 'other_option': 'value2'})
+
+    ... return this:
+
+        (
+            (('my_option', 'sub_option'), 'value1'),
+            (('other_option'), 'value2'),
+        )
+
+    Raise ValueError if an override can't be parsed.
+    '''
+    prepared_values = []
+
+    for argument_name, value in global_arguments.__dict__.items():
+        try:
+            if value is None:
+                continue
+
+            keys = tuple(argument_name.split('.'))
+            option_type = type_for_option(schema, keys)
+
+            # The argument doesn't correspond to any option in the schema, so ignore it. It's
+            # probably a flag that borgmatic has on the command-line but not in configuration.
+            if option_type is None:
+                continue
+
+            prepared_values.append(
+                (
+                    keys,
+                    value,
+                )
+            )
+        except ruamel.yaml.error.YAMLError as error:
+            raise ValueError(f"Invalid override '{raw_override}': {error.problem}")
+
+    return tuple(prepared_values)
+
+
+def apply_arguments_to_config(config, schema, global_arguments):
+    '''
+    Given a configuration dict, a corresponding configuration schema dict, and global arguments as
+    an argparse.Namespace, set those given argument values into their corresponding configuration
+    options in the configuration dict.
+
+    This supports argument flags of the from "--foo.bar.baz" where each dotted component is a nested
+    configuration object. Additionally, flags like "--foo.bar[0].baz" are supported to update a list
+    element in the configuration.
+    '''
+
+    for keys, value in prepare_arguments_for_config(global_arguments, schema):
+        set_values(config, keys, value)
diff --git a/borgmatic/config/override.py b/borgmatic/config/override.py
index 8a60cb50..0893f669 100644
--- a/borgmatic/config/override.py
+++ b/borgmatic/config/override.py
@@ -1,8 +1,12 @@
 import io
+import logging
 
 import ruamel.yaml
 
 
+logger = logging.getLogger(__name__)
+
+
 def set_values(config, keys, value):
     '''
     Given a hierarchy of configuration dicts, a sequence of parsed key strings, and a string value,
@@ -134,6 +138,9 @@ def apply_overrides(config, schema, raw_overrides):
     '''
     overrides = parse_overrides(raw_overrides, schema)
 
+    if overrides:
+        logger.warning("The --override flag is deprecated and will be removed from a future release. Instead, use a command-line flag corresponding to the configuration option you'd like to set.")
+
     for keys, value in overrides:
         set_values(config, keys, value)
         set_values(config, strip_section_names(keys), value)
diff --git a/borgmatic/config/schema.yaml b/borgmatic/config/schema.yaml
index 13ab0686..3c1bb20f 100644
--- a/borgmatic/config/schema.yaml
+++ b/borgmatic/config/schema.yaml
@@ -36,9 +36,14 @@ properties:
             properties:
                 path:
                     type: string
+                    description: The local path or Borg URL of the repository.
                     example: ssh://user@backupserver/./{fqdn}
                 label:
                     type: string
+                    description: |
+                        An optional label for the repository, used in logging
+                        and to make selecting the repository easier on the
+                        command-line.
                     example: backupserver
         description: |
             A required list of local or remote repositories with paths and
diff --git a/borgmatic/config/validate.py b/borgmatic/config/validate.py
index c80cee4d..35c8e809 100644
--- a/borgmatic/config/validate.py
+++ b/borgmatic/config/validate.py
@@ -4,7 +4,7 @@ import os
 import jsonschema
 import ruamel.yaml
 
-import borgmatic.config
+import borgmatic.config.arguments
 from borgmatic.config import constants, environment, load, normalize, override
 
 
@@ -84,13 +84,15 @@ def apply_logical_validation(config_filename, parsed_configuration):
             )
 
 
-def parse_configuration(config_filename, schema_filename, overrides=None, resolve_env=True):
+def parse_configuration(config_filename, schema_filename, global_arguments, overrides=None, resolve_env=True):
     '''
     Given the path to a config filename in YAML format, the path to a schema filename in a YAML
-    rendition of JSON Schema format, a sequence of configuration file override strings in the form
-    of "option.suboption=value", and whether to resolve environment variables, return the parsed
-    configuration as a data structure of nested dicts and lists corresponding to the schema. Example
-    return value:
+    rendition of JSON Schema format, global arguments as an argparse.Namespace, a sequence of
+    configuration file override strings in the form of "option.suboption=value", and whether to
+    resolve environment variables, return the parsed configuration as a data structure of nested
+    dicts and lists corresponding to the schema. Example return value.
+
+    Example return value:
 
         {
             'source_directories': ['/home', '/etc'],
@@ -113,6 +115,7 @@ def parse_configuration(config_filename, schema_filename, overrides=None, resolv
     except (ruamel.yaml.error.YAMLError, RecursionError) as error:
         raise Validation_error(config_filename, (str(error),))
 
+    borgmatic.config.arguments.apply_arguments_to_config(config, schema, global_arguments)
     override.apply_overrides(config, schema, overrides)
     constants.apply_constants(config, config.get('constants') if config else {})