The Associated Press investigation on drinking water contamination by pharmaceuticals is a recent installment to the ongoing research about this topic. The U.S. government as well as other scientists have been studying this issue for some time. Here are some interesting links about the topic:
EPA information on Pharmaceuticals and Personal Care Products in the Environment (PPCPs): Frequently Asked Questions about PPCPs in the environment and basic introduction.
USGS What's In Our Wastewater and Where Does It Go? an array of studies and articles on contaminants in wastewater. "The U.S. Geological Survey (USGS) has implemented a national reconnaissance to provide baseline information on the environmental occurrence of "emerging contaminants" such as human and veterinary pharmaceuticals (e.g., fluoxetine and lincomycin), industrial and household wastewater products (e.g., p-nonyphenol and triclosan), and reproductive and steroidal hormones (e.g., equilenin and progesterone) in water resources."
The Environmental Working Group: A national assessment of tap water quality.