Bonner was born in Wichita, Kansas. He grew up in Wichita where his father practiced law and his mother was a school teacher. He credits his mother for infusing him with a strong commitment to public service. He received a Bachelor of Arts degree from the University of Maryland, College Park in 1963 and a Juris Doctor from Georgetown University Law Center in 1966. He was a law clerk for Albert Lee Stephens, Jr. of the United States District Court for the Southern District of California from 1966 to 1967. He was on active duty in the United States Navy’s Judge Advocate General Corps from 1967-1971, rising to the rank of Lieutenant Commander, USNR. During that time, he served for nearly two years on an aircraft carrier, the USS Franklin D. Roosevelt (CVA-42). He was an Assistant United States Attorney for the Central District of California from 1971 to 1975, and then went into private practice in Los Angeles for nine years. Afterwards he became the United States Attorney for the same district in 1984. As a United States Attorney, he worked closely with the Drug Enforcement Administration (DEA) on two record-breaking money laundering cases, Operations Pisces and Polar Cap, and had led the prosecution team against the killers of a DEA special agent.
On February 28, 1989, Bonner was nominated by President George H. W. Bush to be a United States District Judge of the United States District Court for the Central District of California, to a seat vacated by Judge Pamela Ann Rymer. He was confirmed by the United States Senate on May 18, 1989, and received commission on May 24, 1989. Bonner resigned on August 12, 1990, to be reassigned to a new position.
On May 11, 1990, President Bush nominated him to be Administrator of the DEA. He was confirmed by the United States Senate on July 27, 1990, and sworn in as the DEA's fifth Administrator on August 13, 1990. Bonner served as Administrator from August 16, 1990, to October 31, 1993.
In 1992, Administrator Bonner issued a ruling that incorporated the FDA’s “safe and effective” standard to evaluate marijuana. After reviewing the record, he found that there were no valid scientific studies that indicated that smoking marijuana was safe and effective for any medical purpose. On that basis, he denied an application for the removal of cannabis from Schedule I of the Controlled Substances Act, stating that, "Those who insist that marijuana has medical uses would serve society better by promoting or sponsoring more legitimate scientific research, rather than throwing their time, money and rhetoric into lobbying, public relations campaigns and perennial litigation."
In November 1993, just after leaving his post as head of the DEA, Bonner appeared on 60 Minutes and criticized the CIA for permitting a drug shipment of one ton of pure cocaine to be smuggled into the U.S. without first notifying and securing the approval of the DEA. From 1993 to 2001, Judge Bonner was a partner in the Los Angeles and Washington, D.C. law firm Gibson, Dunn & Crutcher, an international law firm. His practice focused on business and white-collar crime matters, complex civil cases, internal corporate investigations, and corporate compliance programs. Among his clients were Occidental Petroleum Chairman Ray Irani, French entrepreneur Francois Pinault, former President of Serbia Milan Panic, ConAgra, Waste Management, Inc., the California Institute of Technology, and the cities of Long Beach and Thousand Oaks. He also defended Heidi Fleiss in her federal tax evasion prosecution and personally prosecuted the first FBI Agent charged with espionage.
On June 24, 2001, President George W. Bush nominated Bonner as Commissioner of the United States Customs Service, later known as U.S. Customs and Border Protection, and he was confirmed on September 19, 2001, a little more than a week after the September 11 attacks. During his time as Commissioner, Bonner implemented far-reaching security changes, including the establishment of the National Targeting Center, the Container Security Initiative (CSI), and the Customs-Trade Partnership Against Terrorism (C-TPAT). He announced his resignation from that position on September 28, 2005, having served four years which included the creation of the Department of Homeland Security and the transfer of the Customs Service to that department, and retired on November 25, 2005.
Bonner was hired by Representative Jerry Lewis in 2006 after Lewis was linked to an investigation being conducted by the U.S. Department of Justice (see Jerry Lewis - Lowery lobbying firm controversy). Lewis did not ultimately face charges. On August 12, 2007, Bonner was named by the Rudy Giuliani Presidential Committee as a member of the campaign's "Immigration Advisory Board". Bonner has continued his involvement with border security and immigration, and was appointed to the Homeland Security Advisory Council (HSAC) Southwest Border Task Force by Homeland Security Secretary Janet Napolitano in 2009, and was appointed to the HSAC Integrity Advisory Panel by Homeland Security Secretary Jeh Johnson in 2015. In addition, he has also served on the Council on Foreign Relations task forces on U.S. Immigration Policy and North America, is the co-chair of the Pacific Council task force on U.S.‑Mexico border issues, and is a member of the Civilian Oversight Commission for the Los Angeles County Sheriff’s Department. He retired as a partner of Gibson, Dunn & Crutcher to become a Senior Principal of Sentinel Strategy & Policy Consulting, a Washington, D.C.-based homeland security consulting firm. He also heads Bonner ADR Services and serves as an arbitrator for high stakes disputes.
Bonner, who runs three miles a day, enjoys playing tennis and chess, a game he mastered while serving in the United States Navy on board an aircraft carrier.