The United States Geological Survey (USGS) maintains two stream gauges along Canajoharie Creek.
The upper one, in operation since 1993, is located 10 feet (3.0 m) upstream from the bridge on Mc Ewan Road, and 2.3 miles (3.7 km) southwest of the village of Canajoharie.
The lower one is located at the creek's mouth.

The upper station had a maximum discharge of 5,850 cubic feet (166 m³) per second and a gauge height of 10.76 feet (3.28 m) on August 28, 2011, as Hurricane Irene passed through the area.
It had minimum discharge of .23 cubic feet (0.0065 m³) per second and a gauge height of 1.26 feet (0.38 m) on September 10, 2015.
The upper station had a maximum water temperature of 99 °F (37 °C) on July 15, 1995.

There was formerly a stream gauge just east of Sprout Brook located where Vandeusenville Road crosses the creek.
It was in service from June 14, 1994 to December 19, 1995.
This station had a maximum discharge of 154 cubic feet (4.4 m³) per second on June 3, 1995, and a minimum discharge of .49 cubic feet (0.014 m³) per second on September 6, 1994.
Another former stream gauge was located southwest of the hamlet of Sprout Brook where Mill Road crosses the creek.
It was in service from September 7, 1994 to August 22, 1995.
This station had a maximum recorded discharge of 3.53 cubic feet (0.100 m³) per second on September 7, 1994, and a minimum recorded discharge of .70 cubic feet (0.020 m³) per second on August 22, 1995.

The USGS has been sampling water quality in this watershed since 1994.
The DEC rates the Canajoharie Creek's water quality at Class C, suitable for fishing and non-contact human recreation.
The United States Geological Survey (USGS) maintains two stream gauges along Canajoharie Creek. The upper one, in operation since 1993, is located 10 feet (3.0 m) upstream from the bridge on Mc Ewan Road, and 2.3 miles (3.7 km) southwest of the village of Canajoharie. The lower one is located at the creek's mouth.
The upper station had a maximum discharge of 5,850 cubic feet (166 m³) per second and a gauge height of 10.76 feet (3.28 m) on August 28, 2011, as Hurricane Irene passed through the area. It had minimum discharge of .23 cubic feet (0.0065 m³) per second and a gauge height of 1.26 feet (0.38 m) on September 10, 2015. The upper station had a maximum water temperature of 99 °F (37 °C) on July 15, 1995.
There was formerly a stream gauge just east of Sprout Brook located where Vandeusenville Road crosses the creek. It was in service from June 14, 1994 to December 19, 1995. This station had a maximum discharge of 154 cubic feet (4.4 m³) per second on June 3, 1995, and a minimum discharge of .49 cubic feet (0.014 m³) per second on September 6, 1994. Another former stream gauge was located southwest of the hamlet of Sprout Brook where Mill Road crosses the creek. It was in service from September 7, 1994 to August 22, 1995. This station had a maximum recorded discharge of 3.53 cubic feet (0.100 m³) per second on September 7, 1994, and a minimum recorded discharge of .70 cubic feet (0.020 m³) per second on August 22, 1995.
The USGS has been sampling water quality in this watershed since 1994. The DEC rates the Canajoharie Creek's water quality at Class C, suitable for fishing and non-contact human recreation.
Canajoharie Creek