"Uglies" by Scott Westerfield - genetically engineered white orchids crowd out other species and turn huge acreages into wastelands.
I'll put in a plug for having your students research the subject in question from whatever novel you're looking at, especially if the novel was written some time ago. I find that fiction often skims over what things are really like, how people really handle things. Take the above example in Uglies. It's really not very realistic, because in fact nature is incredibly resilient and you wouldn't get one monoculture for hundreds of years, especially from a small plant like that. you could get problems for sure, just not how it's described (at one point a character says maybe nature would finally come back in 1,000 years...). But you could read that book, and then look at how introduced species are causing problems, because they do, like kudzu in the southeast U.S., or tamarisk in the desert southwest along the Rio Grande, where it sucks up water and competes better than other trees, or fish in the Great Lakes (forget the species). Some of the biggest impacts are actually economic. Kids tend to see things as black and white, and fiction doesn't explore the complexities of the science, or even of the regulations in place or who is fighting for what and why. Improper disposal of hazardous waste used to be a huge problem, but now it isn't really, because there are very good laws in place, and people can go to jail (the problem now is dealing with haz waste that was dumped 40 years ago, but that's a different issue - one of cleanup and who pays for it when you don't even know who dumped it).
All that said, I think fiction can be a great jumping off place to look at issues - just don't leave them thinking fiction is true.
I'm off my soapbox. Have fun with the project!