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Flooding
The Mohawk River has a relatively long record of flooding that has been documented back to settlement in the 17th century. The average volume of water that flows through the Mohawk is about 5.21 km3 every year. Much of the water flows through the watershed in the spring as snow melts rapidly and enters the tributaries and the main trunk of the river. There is a long record of significant and damaging floods along the entire length of the river.

Because the river and its tributaries typically freeze in the winter, the spring melt is commonly accompanied by ice floes that get stuck and jammed along the main trunk of the river. This annual spring breakup typically occurs in the last few weeks of March, although there are numerous floods that have occurred before or after this time, such as in 2018 when the ice jam breakup happened in late February after record warm weather in the region. These ice jams can cause considerable damage to structures along the riverbanks and on the floodplain. The most severe flood of record on the main trunk of the Mohawk River was the spring breakup flood that occurred from 27 to 28 March 1914. This flood caused a tremendous amount of damage to the infrastructure because it was a spring breakup flood with enormous amounts of ice. Ice jams of some significance occur about every other year.

One major flood on the Mohawk was from June 26-29, 2006, during the Mid-Atlantic United States flood of 2006. Flooding was caused by a stalled frontal system that resulted in 50 to 330 mm of rain across central New York and widespread flooding occurred in the Mohawk, Delaware, and Susquehanna watersheds. Across the state, this event caused over $227 million in damage and resulted in the loss of four lives. This flooding was acute in the upper parts of the Mohawk watershed.

The Mohawk River also saw significant flooding during the weeks between August 21, 2011 and September 5, 2011 due to torrential rains experienced from Hurricane Irene and Tropical Storm Lee. Many of the Mohawk Barge Canal locks sustained major damage, especially near Waterford and Rotterdam Junction.

Another major flood was on June 28, 2013. It was caused by heavy rain that had fallen in the region for weeks. On the night of June 27, 2013, the Jordanville area reported that 4 inches of rain fell in one hour. The next day, the Mohawk River flooded the valley, residents were stranded and without power for about a week. There was considerable damage everywhere, especially Mohawk and Fort Plain.

Discharge
The one located by the Rome Fish Hatchery, about 1.0 mi downstream from Delta Dam has been in operation continuously since October 1927, and before that took monthly measurements from July 1921 to September 1927. The maximum discharge was 8560 cuft per second on October 2, 1945, and the minimum discharge was 15 cuft per second in March, October and November of 2002.

The one 2 mi upstream from the mouth at the School Street powerplant in Cohoes, has been in operation since 1917. The maximum discharge was 143000 cuft per second on March 6, 1964, caused by the of release of an ice jam. The minimum discharge was 6 cuft per second on September 18, 1941. Before records were taken, an extreme flood occurred between 1860 and 1865, with a depth of 12 ft on the Cohoes Dam and a peak discharge estimated to be at least 200000 cuft per second.