Courts are already clogged, and underpaid attorneys are turning to the private sector.

Tens of thousands of legal cases ranging from minor thefts to civil disputes to murder are stuck in limbo in state courts around the country, a situation that has left some defendants waiting in jail and strained prosecutors’ and defense attorneys’ ability to do their jobs.

Large cities face some of the steepest challenges. Places like New York, Chicago and San Francisco handle large volumes of cases each year and have seen rates of some violent crimes soar. They have also been home to stringent public health measures that limited court operations.

Many courts had to shut down in-person proceedings for weeks or months at a time over the last couple of years, most recently when the Omicron variant swept through the country. Even when courthouses are open, they can host fewer trials due to social distancing requirements.

San Francisco Public Defender Mano Raju has petitioned a California appeals court to address the backlog of trials that has built up since the beginning of the pandemic. According to his office, as of mid-January there were some 250 San Francisco defendants waiting in jail beyond their legally guaranteed deadlines for a speedy trial.

“Those rights don’t mean anything if you don’t have a court where we can actually exercise those constitutional protections,” Mr. Raju said.

A spokesman for the San Francisco Superior Court said, “The court continues its commitment to justice by processing all cases as expeditiously as possible under the difficult circumstances presented by the pandemic.”

Miami-Dade Public Defender Carlos Martinez said staffing shortages have proven a huge barrier to clearing his office’s 16,000 pending cases, with burned-out attorneys being lured to the private sector by law firms whose case loads have also swelled and are able to pay their lawyers more.

Mr. Martinez said he lost more than 60 attorneys during the prior fiscal year, or 35% of his staff. That means the remaining lawyers are juggling even larger caseloads, often with less experience.

Prosecutors meanwhile say they are concerned about a lack of accountability for people who have committed crimes. And the delay in resolving cases may mean that people who need court-ordered drug or mental health treatment aren’t getting it. “Not having accountability, even for low-level nonviolent crimes, I don’t think is a good thing for society,” said Erie County District Attorney John Flynn, president-elect of the National District Attorneys Association.

Nationally, the number of criminal jury trials in state courts dropped by nearly 60% in 2020 compared with a year earlier, according to the National Center for State Courts. Roughly 1.3 million more cases came into the system in 2020 than were resolved.

Many court systems and judges waived speedy trial deadlines specified by state statutes, often over the objections of defendants as the months dragged on. Legal observers say the right to a speedy trial has never been suspended on such a widespread basis for such an extended period. “This is something we really haven't seen in modern times,” said Jenny Carroll, director of the Arthur Liman Center for Public Interest Law at Yale Law School.

William Cogman, 48, was arrested for assault and weapons possession charges in November 2020. He pleaded not guilty in San Francisco Superior Court and has spent more than 15 months in jail waiting on his case. His original deadline to face a trial, according to the state’s speedy trial rules, was more than a year ago.

During his time in detention, Mr. Cogman said he developed chronic obstructive pulmonary disease and now struggles to breathe, his voice having evaporated to a whisper. Because of Covid-related safety precautions at the jail he said he has only been allowed to leave his cell for one hour a day, leaving him to choose between calling his lawyer or family members or taking a shower. He has taken a tentative plea deal because he sees no other end in sight.

“I’ve been holding on and holding on and holding on,” he said.