First, you should ensure, that no one is working with aqua.
For JIRA-Sync users:
In case you have configured one or more JIRA-Syncs, please stop all running JIRA-Syncs using the aqua Sync Configurator before you stop the aqua server. Please note which Syncs have been active. After having terminated the Syncs, please wait ~10 minutes. The Syncs will need this time to terminate properly.
For automation agent users:
Please stop all automation agents that are connected to your the aqua Server.
In order to stop your aqua Server, please open IIS-Manager on Microsoft Server.
You should click on aquaAPIPool and stop it with the button on the right hand side. Repeat this process with aquaFileServerPool and aquaWebservicePool and (if installed) aquaWebNGAppPool.
Your aqua Server has stopped now.