Pesticides like the neurotoxic bug-killer chlorpyrifos are widespread in the waters of the Chesapeake Bay, threatening the progress of a landmark plan to clean up pollution in the Mid-Atlantic watershed, according to a scientist in the region.

Chlorpyrifos, first registered as a pesticide in 1965, is the subject of legal battle between environmentalists who want to ban it for its effects on brain development in children and fetuses, and the Environmental Protection Agency, which says it’s an important pesticide to protect crops.

The chemical is commonly found in the bay’s waters and poses a...