At noon on the first Tuesday of February 2013, Jonathan Lippman, the chief judge of New York State, spoke to the most powerful people in state government about his “critically important concern” over a practice that, he said, “strips our justice system of its credibility and distorts its operation.”

That would be holding people accused of a crime, but not convicted, in jail on bail even though they were not threats to the public or likely to flee. That day, as Judge Lippman delivered the remarks in Albany, part of his annual state of the judiciary address, the attorney general and leaders of the State Legislature were in the audience. He urged legislative reforms in the pretrial detention system so that it would be more fair and less costly.

On the day of the judge’s speech, Kalief Browder was locked in a jail on Rikers Island, 150 miles away. It was his 997th consecutive day in custody as he awaited trial on a charge that he stole a backpack in the Bronx. His mother had been unable to come up with $3,000 bail.

Mr. Browder, arrested when he was 16, spent more than 1,000 days in jail before the charges were dropped, about 800 of them in solitary confinement. Insisting that he was innocent, he refused plea bargains that would have allowed him to go home, even as his case was delayed month after month. Videotapes show him being beaten by guards and other prisoners. He tried to commit suicide several times. His story was chronicled last year by Jennifer Gonnerman in The New Yorker, who reported that jailhouse isolation haunted him at work and at home.