If you are using the Encryption-Feature for Drives / Partitions in OS X 10.11 “El Capitan” it could be bugging to get a prompt to unlock each after the Login.

File Vault Dialog

A quick way to stop OS X from auto-mounting encrypted Filesystems would be to disable the respective Daemon. 

Fire up a Terminal Window (Applications>Utilities>Terminal) and enter the following commands:

sudo mkdir /System/Library/LaunchDaemons.Disabled

This will create a directory where we will move the Daemon to prevent it from autoloading. Finally we will move the Daemon:

sudo mv /System/Library/LaunchDaemons/com.apple.corestorage.corestoraged.plist /System/Library/LaunchDaemons.Disabled/

Reboot OS X and you are done.

To unlock your Drives / Partitions open the Disk Utility (Applications>Utilities>Disk Utility) and select the Device you want to unlock. Select “File>Unlock…” and you will be prompted for the Password.