asp.net web.config impersonation vs application pool identity
When you access resources on the server the user will be the one specified on the impersonation configuration NOT the one on the application pool
Impersonation enabled for a specific identity. In this instance, ASP.NET impersonates the token generated using an identity specified in the Web.config file.
<identity impersonate="true" userName="domain\user" password="password" />Impersonation enabled. In this instance, ASP.NET impersonates the token passed to it by IIS, which is either an authenticated user or the anonymous Internet user account.
<identity impersonate="true" />Source: MSDN
In case you're interested, here you have an article with a Identity matrix for different impersonate scenarios.
And yes, you can impersonate programatically as Alex Dn said