Is there a way to know remote desktop password in which AA is running

Not sure I understand your question. You mean the bot is already running and logging into a remote desktop? If so, it must contain the credentials in the bot itself, either plain text or in the credential vault.

Bot is required to login into web application, whose credentials are same as sys(remote desktop) Username and password. I retrieved the username using env variables. Is there any way to retrieve system password.

Again, how did you set the credentials for the remote desktop? Are they in the bot in plain text, are they in the Credential Vault, or did you set them under the User account in the Device Login Credentials section? Where you configured this will determine whether or not they can be retrieved. 

It is runner machine, it auto logs in when the bot runs. I have multiple runners, I need the password of the machine on which the bot runs.
Is there a way to know runner machine password in which AA is running

Sorry, it sounds like someone set that in the Device Login Credentials section in the Control Room. To my knowledge it cannot be retrieved through the UI or the API.