According to the United States Census Bureau, the town has a total area of 32.3 square miles (84 kmē), of which 31.8 sq mi (82 kmē) is land and 0.6 sq mi (1.6 kmē) is water, comprising 1.76% of the town. The highest point in Hollis is the summit of Birch Hill, at 821 feet (250 m) above sea level, located near the town's western border.
The Nashua River flows through the southeast corner of the town out of Pepperell, Massachusetts and into Nashua. The Nissitissit River flows through the western part of the town. Hollis lies fully within the Merrimack River watershed
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