[3] The Mexico-United States border runs along the south face of the mountain.

[3] On March 16, 1991, a Hawker Siddeley HS-125 airplane carrying seven members of singer Reba McEntire's band, plus her business manager and two pilots, crashed into the side of the mountain after taking off from nearby Brown Field Municipal Airport, killing all ten on board.

The plant life in Otay Mountain "burned completely" in 2003, and another wildfire happened later in 2007.

The border fence has received criticism for its effects on nature and wilderness.

[7] In particular, the construction was criticized by author Rob Davis for creating a harsh environment for a species of butterfly due to dust being kicked up by trucks.