WOBURN — Investigators tracking drug activity around Main Street in Woburn Thursday evening thought they were watching a typical narcotics deal.

It started at about 5 p.m. as officers observed a 30-year-old man with a history of drug arrests take a short ride in a Chevrolet Malibu, according to a police report.

That man, Thomas C. Donaghey, got out of the Malibu on Stoddard Street, saw a detective, and took off running, police said.

At about the same time, an unmarked police cruiser tried to pull over the car, which fled as the driver allegedly swallowed drugs and the female passenger threw money and a cellphone out the window, the report said.

The chase spanned a little more than a half-mile and reached estimated speeds of 45 to 55 miles per hour in an area where the speed limit is 30, according to police.

The Malibu hit a dead end on Eastern Avenue, ending the pursuit, and that is when officers learned a 4-year-old boy had been in the back seat the entire time. He was not in a car seat, police said.

“The child was crying hysterically, with streams of tears coming from his eyes when I first observed him,’’ Woburn Detective Sergeant Brian McManus wrote in the report.

Officers arrested the driver, Raymond Carrion Sanchez, 32, the boy’s mother, Josmil Rosario, and Donaghey, who was described in the report as the initial target of the drug probe.

Sanchez, who lives in Lawrence, was arraigned Friday morning in Woburn District Court, where not-guilty pleas were entered on his behalf to charges of reckless endangerment of a child, conspiracy to violate drug law, obstruction of justice, and several motor vehicle offenses.

Middlesex Assistant District Attorney A.J. Chalifour said Sanchez’s alleged conduct posed “significant danger’’ to the boy and pedestrians walking on city streets as the chase unfolded.

A spokeswoman for the state Department of Children and Families said the agency is investigating the case.

Prior to the chase, investigators believe Donaghey was in Sanchez’s car to pay $300 for heroin and cocaine, though the drugs were to be delivered to another person, the report said.

Donaghey’s lawyer, Raymond Weicker, denied the allegation, saying his client was paying off a debt for heroin that had already been provided.

Police also alleged Donaghey, who was captured after a foot chase, had a partial pill of Suboxone with him and charged him with illegal drug possession.

Weicker said Donaghey, of Woburn, has a prescription for the Suboxone, but he could not immediately produce the document Friday. The drug is used to treat opiate addiction.

Superior Court Judge Kimberly S. Budd set Donaghey’s bail at $100.

Sanchez’s lawyer, Paul Lawton, said investigators did not find drugs on Sanchez or in his vehicle and asked Budd to set his bail at $750.

“There’s no direct evidence to show Mr. Sanchez was involved in the sale,’’ Lawton said.

Budd set bail for Sanchez at $20,000. She also revoked his bail on a pending case in Somerville District Court, where he is accused of assault and battery on a police officer, witness intimidation, and conspiracy to violate drug law.

Budd, who was nominated by Governor Charlie Baker this week for a seat on the state Supreme Judicial Court, presided over the case because a district judge was not available.

Rosario, 25, who lives in Cambridge, was charged with two counts of obstruction of justice, conspiracy to violate drug law, and reckless endangerment of a child, the report said. She was released on $250 bail Thursday and is scheduled to be arraigned Monday, police said.

A woman who answered the door Friday at an address for Rosario said the residence was a shelter and declined to comment.

Laura Crimaldi can be reached at laura.crimaldi@globe.com. Follow her on Twitter @lauracrimaldi.