SharePoint security is a broad topic. In SharePoint, you can create groups, add roles, and set permissions. You can add users to those groups and set permissions for sites and apps. The Users and Permissions section of the Site Settings page is where you administer SharePoint security.
The Users and Permissions section contains links to the following settings pages:
People and Groups: Click to view settings for all the users in your site. Using the People and Groups settings page, you can create new groups, add and remove users from groups, and set permissions for groups.
Site Permissions: Click to see a page where you can create groups, add roles, change access request settings, and view current roles. In addition, you can add, edit, view, and remove permissions from users.
Site Collection Administrators: Click this link to set which users have site collection administrator permissions. Site collection administrators have permissions to all the sites contained in the Site Collection. This could be many sites, depending on how your SharePoint farm is set up.
If you’re a site collection administrator, be very careful who you give this permission to. (This link does not appear if you’re not already a site collection administrator on the site.)
Site App Permissions: Click to provide permissions to the site for SharePoint apps. This is important for third-party apps that you install on the site that need to access your data.
SharePoint security can take some time to comprehend. Sometimes things just don’t seem to work the way they should.