An estimated 100 million treatments are prescribed every year in Scotland.
After a pill passes through a person’s body, some of its compounds reach rivers, lochs and the sea because waste water plants cannot filter them out.
While the project team say there is no evidence of a risk to the public, they warn of possible threats to marine wildlife.
The One Health Breakthrough Partnership has been set up to investigate the scale of the problem in Scotland, indentify “greener” pharmaceuticals and ways of reducing the amount of compounds reaching natural watercourses.
These potential solutions include using bark, or grain left as a by-product of the whisky distilling industry, to absorb the material from waste water.
The project is examining the issue in detail in a pilot at Wick’s Caithness General Hospital. This work has already given an award from international charity, the Alliance for Water Stewardship.
But Prof Stuart Gibb, of the University of the Highlands and Islands, a project partner, said studies have suggested threats to wildlife.
He said research in North America had found some pharmaceutical compounds causing changes to the development of sexual organs in male fish.
Prof Gibb told BBC Radio Scotland’s Brainwaves programme: “This is not pollution by a conventional route.
“These drugs are simply doing what we’ve chosen them to do. It’s just that they are working in the wrong place on the wrong species.”
Dr Karin Helwig, a lecturer at Glasgow Caledonian University, added: “There is still quite a lot we don’t know about how the drugs behave in rivers, lochs and the sea, how long does it take for them to break down or do they not break down at all.”
Assessments made as part of the work at Caithness General to look for eight different pharmaceuticals in waste water from the hospital found seven of them.
Scottish Water said waste water treatment plant processes have been successful in filtering out some compounds, but not others before the treated water is discharged as effluent.