[2] In 1986, she and Andrew Schneider won the Pulitzer Prize for Specialized Reporting for a series titled "The Challenge of a Miracle: Selling the Gift."
Flaherty and Schneider began publishing the 13-article series in November 1985 after 10 months of investigation into the United States's kidney transplant system and its abuse by wealthy foreign nationals, who bypassed the long wait lists.
She was a finalist for the 1995 Pulitzer Prize for Investigative Reporting with Keith A. Harriston for a series of articles on the hiring practices of the Washington D.C. Police Department.
[6] In 2001 Flaherty, along with Joe Stephens, Deborah Nelson, Karen DeYoung, John Pomfret, Sharon LaFraniere and Doug Struck, wrote a six-part Washington Post investigative series titled "The Body Hunters," on American drug companies conducting tests in Third World countries.
[7] Other notable stories Flaherty has worked on include a 2001 report on faulty testing of the Bell Boeing V-22 Osprey Marine helicopter and a 2013 exposé of massive losses from fraud and embezzlements at nonprofit organizations.