The newspaper found that half or more of the graduates of some schools earn less than a C average in their first year of college.
Raymund Paredes, Texas' higher education commissioner, told the newspaper that many students are "stunned" when they get to college.
While students at low-performing schools struggle, graduates of top schools don't necessarily fare better.
The newspaper found that five of the 12 students who graduated from Dallas' School for the Talented & Gifted in 2007 and went on to a four-year college earned less than a C average.
Alice Black, executive principal of Yvonne A. Ewell Townview Center, which includes TAG, said students get used to the closeness of their high school and then have to adjust to a new, big world.
"Once they go off to college, they're not the smart kid anymore," she told the newspaper.
Mary Hendrix, vice president for student access and success, told the newspaper that many students don't learn how to meet deadlines or take major exams because high schools focus on standardized tests.
Some schools let top students skip final exams, but then they don't have any experience in studying for final exams in college that take place within a couple of days of each other, she said.