FLINT, Mich. — It was the Fourth of July, a warm summer night in 2014, but Tim Monahan was shivering in a thick blanket as he watched fireworks from his front yard here. By the next afternoon his temperature had shot to 104.6, and doctors at the hospital he had checked into puzzled over what was wrong.

Two days later, they had an answer: Legionnaires’ disease, a virulent form of pneumonia caused by a type of bacteria that can multiply in water systems. Mr. Monahan, now 58, was given antibiotics and eventually recovered, but his case turned out to be at the leading edge of a Legionnaires’ outbreak that sickened at least 87 people in the Flint region, killing nine of them, from June 2014 through October 2015.

State officials still say they cannot conclusively link the outbreak to Flint’s contaminated water supply, partly because sputum cultures were not collected from patients. But the possibility of a link was raised in internal government emails as early as October 2014, and state officials did not inform the public of the outbreak until last month.

The Legionnaires’ cases started popping up as Flint residents were complaining about the foul-smelling, discolored water flowing into their homes after the city switched to a new water source, the Flint River, in April 2014. Soon they were reporting rashes and stomach ailments, and whistle-blowers eventually pointed to alarming levels of lead in the water supply and in children’s blood.