FLINT, Mich. — Nakiya Wakes could not understand how her wiry, toothy-grinned 6-year-old had gone from hyperactive one school year to what teachers described as hysterical the next. Then, in 2015, the state of Michigan delivered a diagnosis of sorts: Ms. Wakes’s neighborhood’s water — which her son, Jaylon, had been drinking and bathing in for more than a year — was saturated with lead, at some of the highest levels in the city.

Jaylon would cycle through two schools, receive 30 suspensions and rack up 70 unexcused absences. In one of Ms. Wakes’s clashes with Flint Community Schools, she delivered administrators a warning: “You can’t keep suspending him because soon, you’re going to have to suspend the whole school system.”

Five years after Michigan switched Flint’s water supply to the contaminated Flint River from Lake Huron, the city’s lead crisis has migrated from its homes to its schools, where neurological and behavioral problems — real or feared — among students are threatening to overwhelm the education system.

The contamination of this long-struggling city’s water exposed nearly 30,000 schoolchildren to a neurotoxin known to have detrimental effects on children’s developing brains and nervous systems. Requests for special education or behavioral interventions began rising four years ago, when the water contamination became public, bolstering a class-action lawsuit that demanded more resources for Flint’s children.