At the meeting on Monday, committee members were told that locations in Bedford town centre also showed significant contamination despite being miles away from sewage treatment works.
Horn said he was working with the Environment Agency and the University of Birmingham to identify pollution sources.
An Environment Agency spokesperson said: “With our newly created water industry regulation and enforcement teams, we plan to increase the number of compliance inspections of Anglian Water waste water assets each year.”
The Great Ouse river is navigable for 74.8 miles (120.3km) between Bedford and the Wash at King’s Lynn, Norfolk.
During the meeting, covered by the Local Democracy Reporting Service, one councillor raised concerns about people bathing in the river.
Horn said signs had been installed in Felmersham warning of the risks, but they had been “taken down and thrown away, and people went straight back in the river”.
“So you cannot stop people doing it,” he added.
