In 1996, New York flagged Upper Tonawanda Creek as a water-supply concern. 16 years later, NYSDEC removed it from the impaired list after farm BMPs improved water quality

In 1996, New York identified the upper portion of Tonawanda Creek as a priority waterbody because nutrients and sediment from agricultural activities and other nonpoint sources were affecting its use as a water supply.

The New York State Department of Environmental Conservation added the affected section to the state's Priority Waterbodies List that year and later placed it on the Clean Water Act Section 303(d) list of impaired waters in 2004 because of silt and sediment.