Dead Water Zone by Kenneth Oppel

For as long as he can remember, Paul has looked after his younger, weaker brother Sam. But when Sam leaves home to work as a research assistant in Watertown, he disappears into the dark folds of the city's noxious slum. When Paul goes looking for Sam in Watertown, he learns a dark secret: something in the water is changing the residents of Watertown, transforming them into something inhuman. But can Paul reach Sam before the dark waters get to him first?