Guzman is being held in a maximum security prison in New York after he was extradited last month.
The notorious kingpin escaped twice from prison in Mexico, once in a laundry basket and most recently through a tunnel in his cell.
His lawyers say he has been denied marital visits and is largely kept in solitary confinement.
The claims arose at a federal court in Brooklyn at a hearing for Guzman, who has pleaded not guilty to charges that he ran the world's largest drug-trafficking organisation during a decades-long career.
He faces life in prison if convicted.
Guzman's wife Emma Coronel, a 27-year-old former beauty queen and mother of his twins, flew from Mexico to attend the hearing.
His lawyers said it was first time Ms Coronel had seen her husband since his surprise extradition two weeks ago.
Guzman, 59, is reportedly on 23-hour lockdown in a special unit of the Manhattan Correctional Center.
"We understand the need for security but we think it has gone above and beyond," said Michelle Gelernt, one of his court-appointed lawyers.
District Judge Brian Cogan pointed out that the "history of the defendant is somewhat unusual" - a reference to his past escapes - and said the Federal Bureau of Prisons should decide what conditions Guzman faced and who he could see.
Guzman's Sinaloa cartel allegedly smuggled hundreds of tonnes of cocaine, heroin, marijuana and methamphetamines to the US while waging war with other gangs.
The cartel is accused of carrying out thousands of murders and kidnappings, and bribing officials.
Guzman - widely known by his nickname El Chapo, which means "Shorty" - is believed to have amassed a billion-dollar fortune through the drugs trade.
Mexican President Enrique Pena Nieto had initially resisted extraditing him to the US, insisting that he should face justice at home.
But after Guzman was recaptured in January 2016, Pena Nieto changed his mind on extradition and ordered officials to speed up the process.
Mexican drug lord Joaquin "El Chapo" Guzman has complained in court about his conditions of custody in a US jail.