ITACURUÇA, Brazil — Something ominous was happening in the turquoise waters of Sepetiba Bay, a booming port outside Rio de Janeiro. Beginning late last year, fishermen were coming across the scarred and emaciated carcasses of dolphins, sometimes five a day, bobbing up to the surface.

Since then, scientists there have discovered more than 200 dead Guiana dolphins, or Sotalia guianensis, a quarter of what was the world’s largest concentration of the species. The deaths, caused by respiratory and nervous system failures linked to a virus, have subsided, but scientists are working to unravel the mystery behind them.

How, they ask, did a virus that might ordinarily have claimed a handful of dolphins end up killing scores of them? And does part of the answer, scientists and local residents ask, lie in the bay itself, at once a testament to Brazil’s economic power and a portent of environmental risk.