Lake Rotoiti lies in the park's far north and is mainly fed by the Travers River and smaller streams emerging from the Travers Range in the west. Other sources include several creeks arising from the Saint Arnaud Range in the east. At the northern edge, near the town of Saint Arnaud, Rotoiti has two main bays (West Bay & Kerr Bay) which are separated by the Brunner Peninsula. The lake measures 7.5 km in length and is about 2.7 km wide. Its maximum depth is 82 m. John Sylvanus Cotterel, one of the first to see the lake, named it after Arthur Wakefield, another colonist and founder of Nelson. Both were killed in the Wairau Affray in 1843, so the name changed back to its Maori origin.
Lake Rotoroa ('long lake') is estimated to measure nearly 15 km in length and 3 km of maximum width. It is fed by creeks of the Braeburn and Travers Range as well as the D'Urville and Sabine River arising around Spenser mountains. Both lakes have exiting streams that flow into the massive Buller River.
The entire Nelson Lakes region is a complex system of freshwater streams and lakes. Due to their alpine nature and water filtration through greywacke deep within the mountains, both lakes are considered to have a high water quality. Such quality is measured through the tropic level index (TLI) that examines phosphorus and nitrogen levels, as well as clarity and algae deposits. Lake Rotoiti was labeled as microtrophic, meaning the water is of good quality, clear and blue.