Otero grew up in Albuquerque, New Mexico, the daughter of Hispanic grocers without a college education. She majored in physics at the University of New Mexico, graduating in 1991. She earned a master's degree in geophysics from the University of California, San Diego (UCSD) in 1995, and completed her Ph.D. in 2001 in physics education research jointly through UCSD and San Diego State University.