In which season does Debra Morgan discover Dexter's secret?

Debra Morgan discovers Dexter’s secret in season 6.

The revelation occurs in the season-six finale, “This Is the Way the World Ends.” Dexter captures Travis Marshall, the season’s religiously motivated killer, and takes him to the abandoned church where he intends to carry out a ritualized murder. Debra arrives unexpectedly and sees Dexter kill Travis.

Until that moment, Debra knows Dexter as her adoptive brother and a blood-spatter analyst, but she does not know that he has secretly been killing murderers for years. Her discovery is presented as the major cliffhanger of the season and directly drives the conflict of season 7.

Viewers sometimes place the reveal in season 7 because its consequences dominate the next season. However, the actual discovery happens at the end of season 6. It is also more precise to say that Debra witnesses Dexter committing a murder; the full implications of his secret life unfold gradually afterward.