Brain-eating amoebas. Amoebas are common to any open body of fresh water, and attacks like this are rare. Apparently it takes a lot of swallowed water to get these amoebas into your system. Never smart to swallow lake water, I think.
Update: This story appears to have gotten popular again, so I’ve updated the previously dead link to something more updated — this paper on brain-eating amoebas, and a CNN news story on increased amoeba-related deaths in Summer 2007.