I need to change some custom objects permissions for the
Standard User profile. But those checkboxes seem read-only. How can I update these permissions?
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You are limited to the settings that are editable on standard profiles. This includes the Standard User profile, which does not allow you to edit the object level permissions.
You must clone the a standard profile (in this case the Standard User) and then customize your settings with your new Custom Profile.
Your org includes several standard profiles where you can edit a limited number of settings.
Additionally, as @cropredy mentioned, you can use Permission Sets to add additional permissions if you want to keep the same Standard User profile (Note: you cannot remove permissions with Permission Sets).