Some colleges, in an effort to sort through a growing number of applications, are quietly tracking prospective students’ online interaction with the schools and considering it in deciding whom to admit.

Enrollment officers at institutions including Seton Hall University, Quinnipiac University and Dickinson College know down to the second when prospective students opened an email from the school, how long they spent reading it and whether they clicked through to any links. Boston University knows if prospective students RSVP’d...