He was on in the United States Navy Reserve Judge Advocate General Corps from 1967 to 1971, rising to the rank of Lieutenant, USNR.

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.

[1] 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, led the prosecution team against the killers of a DEA special agent, and personally prosecuted the first FBI agent charged with espionage.

[4] As DEA Administrator, Bonner is credited with implementing the Kingpin Strategy, which allows law enforcement to target and attack key vulnerabilities of major transnational drug trafficking organizations.

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.

[2] Among his clients were Occidental Petroleum Chairman Ray Irani, French entrepreneur Francois Pinault, former President of Serbia Milan Panic, ConAgra, Walmart, Waste Management, Inc., the California Institute of Technology, and the cities of Long Beach and Thousand Oaks.

In addition, he has 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, is the chair of the Civilian Oversight Commission for the Los Angeles County Sheriff's Department, and is the co-chair of the International Summit on Borders.